Alignments for a candidate for icd in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Magnetospirillum magneticum AMB-1

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate WP_043743299.1 AMB_RS03135 NADP-dependent isocitrate dehydrogenase

Query= SwissProt::P16100
         (741 letters)



>NCBI__GCF_000009985.1:WP_043743299.1
          Length = 741

 Score = 1117 bits (2890), Expect = 0.0
 Identities = 559/741 (75%), Positives = 633/741 (85%), Gaps = 1/741 (0%)

Query: 1   MSTPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQ 60
           M+T KII+T  DEAPALATYSLLPI++AFTG++G+AVETRDISLAGR+IA FPE LT  Q
Sbjct: 1   MTTAKIIWTKVDEAPALATYSLLPIVQAFTGAAGVAVETRDISLAGRIIANFPENLTPAQ 60

Query: 61  KISDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEK 120
           +I D+LAELG+L   P+ANIIKLPN+SASVPQLKAAIKELQ QGYK+PD+PE+PKTD EK
Sbjct: 61  RIGDELAELGELTLKPEANIIKLPNVSASVPQLKAAIKELQSQGYKIPDFPEDPKTDAEK 120

Query: 121 DVKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGD 180
           ++KAR+ K+ GSAVNPVLREGNSDRRA  SVK +ARK+PHKMGAW+A S+SHVAHM+ GD
Sbjct: 121 ELKARFGKVLGSAVNPVLREGNSDRRAAASVKAFARKNPHKMGAWAASSQSHVAHMNAGD 180

Query: 181 FYGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEI 240
           FYGSEK+  + A   VKIE   KDGS  VLKAKT ++AGE+ID++VMS  ALR F A +I
Sbjct: 181 FYGSEKSVTVAAATDVKIEFHGKDGSIHVLKAKTKLKAGEVIDAAVMSAKALRAFYAEQI 240

Query: 241 EDAKKQ-GVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGD 299
            DAK Q G+LLS+HLKATMMKVSDPIMFG  V+ F+KD   KHA  +K +G +VNNG GD
Sbjct: 241 ADAKSQPGLLLSLHLKATMMKVSDPIMFGHAVTVFFKDVFEKHAAAIKDLGVNVNNGFGD 300

Query: 300 LYARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRD 359
           L A++  LP AK+ EIEADI+A Y   P LAMVNSDKGITNLHVPSDVIVDASMPAMIRD
Sbjct: 301 LIAKLDKLPAAKKAEIEADIKAAYEAGPPLAMVNSDKGITNLHVPSDVIVDASMPAMIRD 360

Query: 360 SGKMWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEE 419
           SG+MWG DGKLHDTKA+IPDRCYA +YQVVI+DCK+HGAFDP TMGSVPNVGLMAQKAEE
Sbjct: 361 SGRMWGTDGKLHDTKAMIPDRCYARMYQVVIDDCKKHGAFDPKTMGSVPNVGLMAQKAEE 420

Query: 420 YGSHDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARA 479
           YGSHDKTF+I ADGVV+V DESG +LLEQ VEAGDI+R CQ KDAPIQDWVKLAV RAR 
Sbjct: 421 YGSHDKTFEIAADGVVQVVDESGAVLLEQKVEAGDIFRACQTKDAPIQDWVKLAVTRARL 480

Query: 480 TNTPAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTI 539
           +NTPA+FWLD  RAHDAQ+IAKVE+YLKD+DT+GLDI I +P EA   SL RIR+G DTI
Sbjct: 481 SNTPAIFWLDKNRAHDAQIIAKVEKYLKDHDTTGLDITIKAPEEAIAVSLERIRKGLDTI 540

Query: 540 SVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYL 599
           SVTGNVLRDYLTDLFPI+ELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQF EEGYL
Sbjct: 541 SVTGNVLRDYLTDLFPILELGTSAKMLSIVPLMAGGGLFETGAGGSAPKHVQQFQEEGYL 600

Query: 600 RWDSLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGS 659
           RWDSLGEFLAL  SLEHL   +KNPKA VLA TLDQA  +ILDNN+SPARKVGE+DNRGS
Sbjct: 601 RWDSLGEFLALGVSLEHLAQTFKNPKAQVLADTLDQANARILDNNRSPARKVGELDNRGS 660

Query: 660 HFYLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPN 719
           HFYLALYWAQALA QT+DKEL A+F  +AKALT+NE KI  EL AAQGKPVD+ GYY PN
Sbjct: 661 HFYLALYWAQALAEQTKDKELAARFAPLAKALTENEDKINAELIAAQGKPVDMGGYYSPN 720

Query: 720 TDLTSKAIRPSATFNAALAPL 740
              TS A+RPSAT NAALA +
Sbjct: 721 DSKTSAAMRPSATLNAALAAI 741


Lambda     K      H
   0.315    0.131    0.374 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1551
Number of extensions: 59
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 741
Length of database: 741
Length adjustment: 40
Effective length of query: 701
Effective length of database: 701
Effective search space:   491401
Effective search space used:   491401
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 55 (25.8 bits)

Align candidate WP_043743299.1 AMB_RS03135 (NADP-dependent isocitrate dehydrogenase)
to HMM TIGR00178 (isocitrate dehydrogenase, NADP-dependent (EC 1.1.1.42))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00178.hmm
# target sequence database:        /tmp/gapView.5639.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00178  [M=744]
Accession:   TIGR00178
Description: monomer_idh: isocitrate dehydrogenase, NADP-dependent
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
          0 1345.7   5.5          0 1345.5   5.5    1.0  1  lcl|NCBI__GCF_000009985.1:WP_043743299.1  AMB_RS03135 NADP-dependent isoci


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_043743299.1  AMB_RS03135 NADP-dependent isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1345.5   5.5         0         0       5     742 ..       3     741 .]       1     741 [] 0.99

  Alignments for each domain:
  == domain 1  score: 1345.5 bits;  conditional E-value: 0
                                 TIGR00178   5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGe 73 
                                               +akii+t  deap+latysllpiv+af+++aG++vetrdislagri+a+fpe lt  q+++d+laelGe
  lcl|NCBI__GCF_000009985.1:WP_043743299.1   3 TAKIIWTKVDEAPALATYSLLPIVQAFTGAAGVAVETRDISLAGRIIANFPENLTPAQRIGDELAELGE 71 
                                               58******************************************************************* PP

                                 TIGR00178  74 laktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlre 142
                                               l+  peaniiklpn+sasvpqlkaaikelq++Gy++pd+pe+pktd+ek++kar+ k++Gsavnpvlre
  lcl|NCBI__GCF_000009985.1:WP_043743299.1  72 LTLKPEANIIKLPNVSASVPQLKAAIKELQSQGYKIPDFPEDPKTDAEKELKARFGKVLGSAVNPVLRE 140
                                               ********************************************************************* PP

                                 TIGR00178 143 GnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketv 211
                                               Gnsdrra ++vk +ark+phkmG+w+a s+shvahm+agdfy+seksv++ aa++vkie+  kdG+  v
  lcl|NCBI__GCF_000009985.1:WP_043743299.1 141 GNSDRRAAASVKAFARKNPHKMGAWAASSQSHVAHMNAGDFYGSEKSVTVAAATDVKIEFHGKDGSIHV 209
                                               ********************************************************************* PP

                                 TIGR00178 212 lkaklklldgevidssvlskkalvefleeeiedakee.gvllslhlkatmmkvsdpivfGhvvrvfykd 279
                                               lkak+kl++gevid++v+s+kal++f++e+i+dak + g+llslhlkatmmkvsdpi+fGh+v vf+kd
  lcl|NCBI__GCF_000009985.1:WP_043743299.1 210 LKAKTKLKAGEVIDAAVMSAKALRAFYAEQIADAKSQpGLLLSLHLKATMMKVSDPIMFGHAVTVFFKD 278
                                               **********************************98759****************************** PP

                                 TIGR00178 280 vfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsd 348
                                               vf kha+ +++lG++v+nG++dl+ak+++lpaakk eiead++++ye +p lamv+sdkGitnlhvpsd
  lcl|NCBI__GCF_000009985.1:WP_043743299.1 279 VFEKHAAAIKDLGVNVNNGFGDLIAKLDKLPAAKKAEIEADIKAAYEAGPPLAMVNSDKGITNLHVPSD 347
                                               ********************************************************************* PP

                                 TIGR00178 349 vivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaq 417
                                               vivdasmpamir+sG+m+g+dgkl+dtka+ipd++ya++yq+vi+dckk+Gafdp tmG+vpnvGlmaq
  lcl|NCBI__GCF_000009985.1:WP_043743299.1 348 VIVDASMPAMIRDSGRMWGTDGKLHDTKAMIPDRCYARMYQVVIDDCKKHGAFDPKTMGSVPNVGLMAQ 416
                                               ********************************************************************* PP

                                 TIGR00178 418 kaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpa 486
                                               kaeeyGshdktfei adGvv+vvd+sG vlle++veagdi+r+cq kdapiqdwvklavtrarls+tpa
  lcl|NCBI__GCF_000009985.1:WP_043743299.1 417 KAEEYGSHDKTFEIAADGVVQVVDESGAVLLEQKVEAGDIFRACQTKDAPIQDWVKLAVTRARLSNTPA 485
                                               ********************************************************************* PP

                                 TIGR00178 487 vfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdl 555
                                               +fwld++rahd+++i+kvekylkdhdt+Gldi i  p +a+  slerir+G dtisvtGnvlrdyltdl
  lcl|NCBI__GCF_000009985.1:WP_043743299.1 486 IFWLDKNRAHDAQIIAKVEKYLKDHDTTGLDITIKAPEEAIAVSLERIRKGLDTISVTGNVLRDYLTDL 554
                                               ********************************************************************* PP

                                 TIGR00178 556 fpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaaslehvavktg 624
                                               fpilelGtsakmls+vplmaGGGlfetGaGGsapkhvqq++ee++lrwdslGeflal+ sleh+a++ +
  lcl|NCBI__GCF_000009985.1:WP_043743299.1 555 FPILELGTSAKMLSIVPLMAGGGLFETGAGGSAPKHVQQFQEEGYLRWDSLGEFLALGVSLEHLAQTFK 623
                                               ********************************************************************* PP

                                 TIGR00178 625 nekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaeal 693
                                               n+ka+vladtld+a  ++ld+++sp+rkvGeldnrgs+fyla ywaq+la qt+dkelaa+fa++a+al
  lcl|NCBI__GCF_000009985.1:WP_043743299.1 624 NPKAQVLADTLDQANARILDNNRSPARKVGELDNRGSHFYLALYWAQALAEQTKDKELAARFAPLAKAL 692
                                               ********************************************************************* PP

                                 TIGR00178 694 tkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnaileal 742
                                               t+ne+ki ael a+qG++vd+gGyy+p++ +t++++rpsat+na+l+a+
  lcl|NCBI__GCF_000009985.1:WP_043743299.1 693 TENEDKINAELIAAQGKPVDMGGYYSPNDSKTSAAMRPSATLNAALAAI 741
                                               **********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (741 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 11.29
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources