Alignments for a candidate for icd in Flavobacterium glycines Gm-149

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Flavobacterium glycines Gm-149

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate WP_066324211.1 BLR17_RS08165 NADP-dependent isocitrate dehydrogenase

Query= SwissProt::P16100
         (741 letters)



>NCBI__GCF_900100165.1:WP_066324211.1
          Length = 744

 Score = 1028 bits (2659), Expect = 0.0
 Identities = 510/733 (69%), Positives = 601/733 (81%), Gaps = 2/733 (0%)

Query: 5   KIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQKISD 64
           KI+YTLTDEAP LATYS LPI++AFT ++GI +ET DIS+A R++A FPE+LT+ Q++ D
Sbjct: 6   KIVYTLTDEAPLLATYSFLPIVEAFTATAGIEIETEDISVAARILANFPEFLTEEQRVKD 65

Query: 65  DLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKDVKA 124
            LAELGKLAT P+ANIIKLPN+SASVPQLK AI ELQ  GY +P+YPE P+ D E  +KA
Sbjct: 66  SLAELGKLATAPEANIIKLPNVSASVPQLKGAIAELQAHGYAVPNYPEAPQNDAETAIKA 125

Query: 125 RYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFYGS 184
           +Y KI GSAVNPVLREGNSDRRAP +VKNYA+ +PH MGAWSADSK+ VA M++GDFYGS
Sbjct: 126 KYAKILGSAVNPVLREGNSDRRAPKAVKNYAKANPHSMGAWSADSKTAVASMESGDFYGS 185

Query: 185 EKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIEDAK 244
           E++  +     VKIE + +DG++TVLKA T ++AGEIIDSSVM  NAL++F+A  I +AK
Sbjct: 186 EQSVTVAEATDVKIEFVGQDGTTTVLKASTPLKAGEIIDSSVMHLNALKSFVAKTIAEAK 245

Query: 245 KQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYARI 304
            QGVLLSVHLKATMMKVSDPI+FG IV  ++ D   K+A +  ++G +  NG+GD+YA+I
Sbjct: 246 AQGVLLSVHLKATMMKVSDPIIFGAIVEVYFADVFAKYAALFAELGVNTKNGLGDVYAKI 305

Query: 305 KTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364
                A++ E++A I       P LAMVNSDKGITNLHVPSDVIVDASMPAMIR SG+MW
Sbjct: 306 AG--NAQEAEVKAAIDQAIENGPALAMVNSDKGITNLHVPSDVIVDASMPAMIRTSGQMW 363

Query: 365 GPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYGSHD 424
             +GK  DT A+IPDR YAGVY   I+ CK+HGAFDPTTMGSVPNVGLMAQKAEEYGSHD
Sbjct: 364 NKEGKQQDTIAIIPDRSYAGVYTATIDFCKKHGAFDPTTMGSVPNVGLMAQKAEEYGSHD 423

Query: 425 KTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATNTPA 484
           KTFQ+  +GVVRV D +G +L+EQ+VEA DI+RMCQAKDAPIQDWVKLAVNRAR +NTPA
Sbjct: 424 KTFQMSTNGVVRVVDVNGNVLMEQTVEANDIFRMCQAKDAPIQDWVKLAVNRARLSNTPA 483

Query: 485 VFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVTGN 544
           VFWLD  RAHD ++I KV++YLKDYDT+ LDIRIL+P+ AT F+L RI +G+DTISVTGN
Sbjct: 484 VFWLDENRAHDRELIVKVQKYLKDYDTTALDIRILNPIAATEFTLDRIIKGQDTISVTGN 543

Query: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRWDSL 604
           VLRDYLTDLFPI+E+GTSAKMLSIVPLM+GGGLFETGAGGSAPKHV+QF+ EGYLRWDSL
Sbjct: 544 VLRDYLTDLFPILEVGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVEQFVTEGYLRWDSL 603

Query: 605 GEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHFYLA 664
           GEFLAL ASLEHLG    N KA+VL+ TLDQA    L N+KSPARKVG+IDNRGSHFYLA
Sbjct: 604 GEFLALGASLEHLGQTLNNEKAIVLSETLDQANDAFLKNDKSPARKVGQIDNRGSHFYLA 663

Query: 665 LYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTDLTS 724
           LYWAQALAAQT+D +LQA F  IAK LT+NE KI  EL  AQGKP +I GYY PN  L S
Sbjct: 664 LYWAQALAAQTKDADLQAIFAPIAKELTENEAKIDAELIGAQGKPQEIGGYYQPNPALVS 723

Query: 725 KAIRPSATFNAAL 737
           KA+RPS TFN  L
Sbjct: 724 KAMRPSTTFNTIL 736


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: 1446
Number of extensions: 52
Number of successful extensions: 3
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: 744
Length adjustment: 40
Effective length of query: 701
Effective length of database: 704
Effective search space:   493504
Effective search space used:   493504
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_066324211.1 BLR17_RS08165 (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.2109254.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 1316.8   7.7          0 1316.6   7.7    1.0  1  NCBI__GCF_900100165.1:WP_066324211.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066324211.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1316.6   7.7         0         0       3     742 ..       2     739 ..       1     741 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1316.6 bits;  conditional E-value: 0
                             TIGR00178   3 tekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGela 75 
                                           t+k+ki+ytltdeapllatys+lpiv+af+a+aGie+et dis+a+rila+fpe+lteeq+v+d+laelG+la
  NCBI__GCF_900100165.1:WP_066324211.1   2 TQKSKIVYTLTDEAPLLATYSFLPIVEAFTATAGIEIETEDISVAARILANFPEFLTEEQRVKDSLAELGKLA 74 
                                           6789********************************************************************* PP

                             TIGR00178  76 ktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrr 148
                                           + peaniiklpn+sasvpqlk ai elq++Gy++p+ype p++d+e +ika+yaki+GsavnpvlreGnsdrr
  NCBI__GCF_900100165.1:WP_066324211.1  75 TAPEANIIKLPNVSASVPQLKGAIAELQAHGYAVPNYPEAPQNDAETAIKAKYAKILGSAVNPVLREGNSDRR 147
                                           ************************************************************************* PP

                             TIGR00178 149 aplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldg 221
                                           ap+avk+ya+ +ph+mG+wsadsk+ va m++gdfy+se+sv++ +a++vkie++ +dG++tvlka+++l++g
  NCBI__GCF_900100165.1:WP_066324211.1 148 APKAVKNYAKANPHSMGAWSADSKTAVASMESGDFYGSEQSVTVAEATDVKIEFVGQDGTTTVLKASTPLKAG 220
                                           ************************************************************************* PP

                             TIGR00178 222 evidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGld 294
                                           e+idssv+  +al+ f+++ i++ak++gvlls+hlkatmmkvsdpi+fG +v v+++dvfak+a+l+ +lG++
  NCBI__GCF_900100165.1:WP_066324211.1 221 EIIDSSVMHLNALKSFVAKTIAEAKAQGVLLSVHLKATMMKVSDPIIFGAIVEVYFADVFAKYAALFAELGVN 293
                                           ************************************************************************* PP

                             TIGR00178 295 venGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmyg 367
                                           ++nGl+d+yaki+   +a++ e++a+++++ e++p lamv+sdkGitnlhvpsdvivdasmpamir+sG+m++
  NCBI__GCF_900100165.1:WP_066324211.1 294 TKNGLGDVYAKIA--GNAQEAEVKAAIDQAIENGPALAMVNSDKGITNLHVPSDVIVDASMPAMIRTSGQMWN 364
                                           ************8..58999***************************************************** PP

                             TIGR00178 368 kdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvv 440
                                           k+gk++dt a+ipd+syagvy a i++ckk+GafdpttmG+vpnvGlmaqkaeeyGshdktf++  +Gvvrvv
  NCBI__GCF_900100165.1:WP_066324211.1 365 KEGKQQDTIAIIPDRSYAGVYTATIDFCKKHGAFDPTTMGSVPNVGLMAQKAEEYGSHDKTFQMSTNGVVRVV 437
                                           ************************************************************************* PP

                             TIGR00178 441 dssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdt 513
                                           d +G+vl+e+ vea+di+rmcq+kdapiqdwvklav+rarls+tpavfwld++rahd+eli kv+kylkd+dt
  NCBI__GCF_900100165.1:WP_066324211.1 438 DVNGNVLMEQTVEANDIFRMCQAKDAPIQDWVKLAVNRARLSNTPAVFWLDENRAHDRELIVKVQKYLKDYDT 510
                                           ************************************************************************* PP

                             TIGR00178 514 eGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGG 586
                                           + ldi+il+p+ at+f+l+ri +G+dtisvtGnvlrdyltdlfpile+Gtsakmls+vplm+GGGlfetGaGG
  NCBI__GCF_900100165.1:WP_066324211.1 511 TALDIRILNPIAATEFTLDRIIKGQDTISVTGNVLRDYLTDLFPILEVGTSAKMLSIVPLMNGGGLFETGAGG 583
                                           ************************************************************************* PP

                             TIGR00178 587 sapkhvqqleeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnr 659
                                           sapkhv+q++ e++lrwdslGeflal+asleh++++ +neka vl++tld+a + +l+++ksp+rkvG++dnr
  NCBI__GCF_900100165.1:WP_066324211.1 584 SAPKHVEQFVTEGYLRWDSLGEFLALGASLEHLGQTLNNEKAIVLSETLDQANDAFLKNDKSPARKVGQIDNR 656
                                           ************************************************************************* PP

                             TIGR00178 660 gskfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrps 732
                                           gs+fyla ywaq+laaqt+d++l+a fa++a+ lt+ne+ki+ael  +qG++ ++gGyy+p+  l++k++rps
  NCBI__GCF_900100165.1:WP_066324211.1 657 GSHFYLALYWAQALAAQTKDADLQAIFAPIAKELTENEAKIDAELIGAQGKPQEIGGYYQPNPALVSKAMRPS 729
                                           ************************************************************************* PP

                             TIGR00178 733 atfnaileal 742
                                            tfn+il+ +
  NCBI__GCF_900100165.1:WP_066324211.1 730 TTFNTILDKI 739
                                           *******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (744 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 39.79
//
[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 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