Alignments for a candidate for icd in Flavobacterium sp. LM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Flavobacterium sp. LM5

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate WP_078212105.1 BXU11_RS05840 NADP-dependent isocitrate dehydrogenase

Query= SwissProt::P16100
         (741 letters)



>NCBI__GCF_002017945.1:WP_078212105.1
          Length = 740

 Score = 1021 bits (2641), Expect = 0.0
 Identities = 512/737 (69%), Positives = 598/737 (81%), Gaps = 2/737 (0%)

Query: 5   KIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQKISD 64
           KI YTLTDEAP LATYS LPI++AFT +S I +ETRDISLAGR++A FPE+L + QK SD
Sbjct: 6   KIFYTLTDEAPLLATYSFLPIVQAFTATSDIEIETRDISLAGRILANFPEFLKEDQKTSD 65

Query: 65  DLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKDVKA 124
            L ELGKLATTP+ANIIKLPN+SASVPQLK AI ELQ  GY +PD+PE+P+T+ EK+ KA
Sbjct: 66  ALLELGKLATTPEANIIKLPNVSASVPQLKTAIAELQAHGYAVPDFPEDPQTEEEKNNKA 125

Query: 125 RYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFYGS 184
           +Y K+ GSAVNPVLREGNSDRRAP +VKNYA+ +PH MG WS++SK+HVA M+ GDFYGS
Sbjct: 126 KYAKVLGSAVNPVLREGNSDRRAPKAVKNYAKANPHAMGVWSSESKTHVASMEQGDFYGS 185

Query: 185 EKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIEDAK 244
           E++  +     VKIE +  DG++TVLKA T ++AGEIIDSSVM+  AL++F+A  IE+AK
Sbjct: 186 EQSVTVSEGTDVKIEFVGADGTTTVLKASTPLKAGEIIDSSVMNIAALKSFVAKTIEEAK 245

Query: 245 KQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYARI 304
            Q +LLSVHLKATMMKVSDPI+FG IV  ++     K+A +  ++  D  NG+GD+YA+I
Sbjct: 246 AQNILLSVHLKATMMKVSDPIIFGAIVEVYFAAVFEKYATLFNELNIDTRNGLGDVYAKI 305

Query: 305 KTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364
              P+  Q E+EA I A  A  P LAMVNSDKGITNLHVPSDVIVDASMPAMIR SG+MW
Sbjct: 306 AGHPQ--QAEVEAAIDAAIANGPALAMVNSDKGITNLHVPSDVIVDASMPAMIRTSGQMW 363

Query: 365 GPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYGSHD 424
             +GK  DT A+IPDRCYAGVY   I+ CK+HGAF PTTMGSVPNVGLMAQKAEEYGSHD
Sbjct: 364 NKEGKSQDTVAIIPDRCYAGVYTATIDFCKKHGAFVPTTMGSVPNVGLMAQKAEEYGSHD 423

Query: 425 KTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATNTPA 484
           KTFQI  +GVVRV +  G +L+EQ V   DI+RMCQAKDAPIQDWVKLAVNRAR + TPA
Sbjct: 424 KTFQIQGEGVVRVVNTEGTVLMEQKVAKNDIFRMCQAKDAPIQDWVKLAVNRARLSATPA 483

Query: 485 VFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVTGN 544
           VFWLD  RAHD+Q+I KVE+YLKDYDT+GLDIRILSP+EAT F+L RI +G DTISVTGN
Sbjct: 484 VFWLDNNRAHDSQLIIKVEKYLKDYDTTGLDIRILSPIEATNFTLERIIKGLDTISVTGN 543

Query: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRWDSL 604
           VLRDYLTDLFPI+E+GTSAKMLSIVPLM+GGGLFETGAGGSAPKHV+QF+EEGYLRWDSL
Sbjct: 544 VLRDYLTDLFPILEVGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVEQFIEEGYLRWDSL 603

Query: 605 GEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHFYLA 664
           GEFLAL ASLEHLG    N KA+VLA  LD AT K L N+KSP+RKVG IDNRGSHFYLA
Sbjct: 604 GEFLALGASLEHLGQTLNNAKAIVLAEALDVATEKFLANDKSPSRKVGGIDNRGSHFYLA 663

Query: 665 LYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTDLTS 724
           +YWA+ALAAQ +D +L+A F+ IA     NE +I  EL  AQGKP  I GYY PN +LTS
Sbjct: 664 MYWAEALAAQDKDADLKAIFSPIATEFIANEAQINSELIGAQGKPQTIGGYYQPNPELTS 723

Query: 725 KAIRPSATFNAALAPLA 741
           KA+RPS TFN  LA LA
Sbjct: 724 KAMRPSTTFNTILAKLA 740


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: 1428
Number of extensions: 39
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: 740
Length adjustment: 40
Effective length of query: 701
Effective length of database: 700
Effective search space:   490700
Effective search space used:   490700
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_078212105.1 BXU11_RS05840 (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.2305172.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 1285.3   3.4          0 1285.2   3.4    1.0  1  NCBI__GCF_002017945.1:WP_078212105.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002017945.1:WP_078212105.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1285.2   3.4         0         0       3     742 ..       2     739 ..       1     740 [] 0.99

  Alignments for each domain:
  == domain 1  score: 1285.2 bits;  conditional E-value: 0
                             TIGR00178   3 tekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGela 75 
                                           t+k+ki ytltdeapllatys+lpiv+af+a++ ie+etrdislagrila+fpe+l e+qk +dal elG+la
  NCBI__GCF_002017945.1:WP_078212105.1   2 TQKSKIFYTLTDEAPLLATYSFLPIVQAFTATSDIEIETRDISLAGRILANFPEFLKEDQKTSDALLELGKLA 74 
                                           6789********************************************************************* PP

                             TIGR00178  76 ktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrr 148
                                           +tpeaniiklpn+sasvpqlk+ai elq++Gy++pd+pe+p+t+eek+ ka+yak++GsavnpvlreGnsdrr
  NCBI__GCF_002017945.1:WP_078212105.1  75 TTPEANIIKLPNVSASVPQLKTAIAELQAHGYAVPDFPEDPQTEEEKNNKAKYAKVLGSAVNPVLREGNSDRR 147
                                           ************************************************************************* PP

                             TIGR00178 149 aplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldg 221
                                           ap+avk+ya+ +ph mG ws +sk+hva m++gdfy+se+sv++ + ++vkie++ +dG++tvlka+++l++g
  NCBI__GCF_002017945.1:WP_078212105.1 148 APKAVKNYAKANPHAMGVWSSESKTHVASMEQGDFYGSEQSVTVSEGTDVKIEFVGADGTTTVLKASTPLKAG 220
                                           ************************************************************************* PP

                             TIGR00178 222 evidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGld 294
                                           e+idssv+   al+ f+++ ie+ak++++lls+hlkatmmkvsdpi+fG +v v+++ vf k+a l+++l +d
  NCBI__GCF_002017945.1:WP_078212105.1 221 EIIDSSVMNIAALKSFVAKTIEEAKAQNILLSVHLKATMMKVSDPIIFGAIVEVYFAAVFEKYATLFNELNID 293
                                           ************************************************************************* PP

                             TIGR00178 295 venGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmyg 367
                                           + nGl+d+yaki+  p+  + e+ea+++++ +++p lamv+sdkGitnlhvpsdvivdasmpamir+sG+m++
  NCBI__GCF_002017945.1:WP_078212105.1 294 TRNGLGDVYAKIAGHPQ--QAEVEAAIDAAIANGPALAMVNSDKGITNLHVPSDVIVDASMPAMIRTSGQMWN 364
                                           *************9885..59**************************************************** PP

                             TIGR00178 368 kdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvv 440
                                           k+gk +dt a+ipd++yagvy a i++ckk+Gaf pttmG+vpnvGlmaqkaeeyGshdktf+i+ +Gvvrvv
  NCBI__GCF_002017945.1:WP_078212105.1 365 KEGKSQDTVAIIPDRCYAGVYTATIDFCKKHGAFVPTTMGSVPNVGLMAQKAEEYGSHDKTFQIQGEGVVRVV 437
                                           ************************************************************************* PP

                             TIGR00178 441 dssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdt 513
                                           +++G vl+e++v+++di+rmcq+kdapiqdwvklav+rarls+tpavfwld++rahd++li kvekylkd+dt
  NCBI__GCF_002017945.1:WP_078212105.1 438 NTEGTVLMEQKVAKNDIFRMCQAKDAPIQDWVKLAVNRARLSATPAVFWLDNNRAHDSQLIIKVEKYLKDYDT 510
                                           ************************************************************************* PP

                             TIGR00178 514 eGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGG 586
                                           +Gldi+ilsp++at+f+leri +G dtisvtGnvlrdyltdlfpile+Gtsakmls+vplm+GGGlfetGaGG
  NCBI__GCF_002017945.1:WP_078212105.1 511 TGLDIRILSPIEATNFTLERIIKGLDTISVTGNVLRDYLTDLFPILEVGTSAKMLSIVPLMNGGGLFETGAGG 583
                                           ************************************************************************* PP

                             TIGR00178 587 sapkhvqqleeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnr 659
                                           sapkhv+q+ ee++lrwdslGeflal+asleh++++ +n+ka vla++ld at+k+l ++kspsrkvG +dnr
  NCBI__GCF_002017945.1:WP_078212105.1 584 SAPKHVEQFIEEGYLRWDSLGEFLALGASLEHLGQTLNNAKAIVLAEALDVATEKFLANDKSPSRKVGGIDNR 656
                                           ************************************************************************* PP

                             TIGR00178 660 gskfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrps 732
                                           gs+fyla+ywa++laaq +d++l+a f+++a  +  ne++i +el  +qG++  +gGyy+p+ +lt+k++rps
  NCBI__GCF_002017945.1:WP_078212105.1 657 GSHFYLAMYWAEALAAQDKDADLKAIFSPIATEFIANEAQINSELIGAQGKPQTIGGYYQPNPELTSKAMRPS 729
                                           ************************************************************************* PP

                             TIGR00178 733 atfnaileal 742
                                            tfn+il+ l
  NCBI__GCF_002017945.1:WP_078212105.1 730 TTFNTILAKL 739
                                           *******977 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (740 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 23.67
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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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 2024 update 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