Alignments for a candidate for icd in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Shewanella sp. ANA-3

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate 7024572 Shewana3_1750 isocitrate dehydrogenase, NADP-dependent (RefSeq)

Query= SwissProt::P16100
         (741 letters)



>FitnessBrowser__ANA3:7024572
          Length = 741

 Score = 1074 bits (2777), Expect = 0.0
 Identities = 534/736 (72%), Positives = 614/736 (83%)

Query: 2   STPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQK 61
           ++P IIYT TDEAPALAT SLLPIIK FT ++G+AVETRDISL+GR+IA FPE LTD QK
Sbjct: 4   NSPTIIYTETDEAPALATLSLLPIIKTFTDAAGVAVETRDISLSGRVIANFPEKLTDAQK 63

Query: 62  ISDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKD 121
           I D LAELG+LA  P+ANIIKLPNISAS+PQLKA I ELQQ+GY +P+YP+EPKTD EK 
Sbjct: 64  IGDHLAELGELANQPEANIIKLPNISASIPQLKACILELQQKGYDIPNYPDEPKTDEEKS 123

Query: 122 VKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDF 181
           +KARYDKIKGSAVNPVLREGNSDRRAPLSVKN+A+K+PH MG W+ +S+SHVAHM  GDF
Sbjct: 124 IKARYDKIKGSAVNPVLREGNSDRRAPLSVKNFAKKNPHSMGKWTKESQSHVAHMSEGDF 183

Query: 182 YGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIE 241
           YGSE++  +    +V I L  KDG   VLK+   + AGEIID+SVMSK AL +F   EI 
Sbjct: 184 YGSEQSVTLANADTVNIVLSQKDGQEVVLKSGLKLLAGEIIDASVMSKKALVSFFEREIA 243

Query: 242 DAKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLY 301
           +AK + VLLS+HLKATMMKVSDPIMFG  V  F+K    KHA +  ++G DVNNG GD+Y
Sbjct: 244 NAKAENVLLSLHLKATMMKVSDPIMFGHAVKVFFKPVFDKHASLFAELGVDVNNGFGDVY 303

Query: 302 ARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSG 361
           A+I +LP   + +IEADI AVYA+RP LAMV+SDKGITNLHVPSD+I+DASMPA IR SG
Sbjct: 304 AKIASLPADVRAQIEADIAAVYAERPALAMVDSDKGITNLHVPSDIIIDASMPAAIRSSG 363

Query: 362 KMWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYG 421
           +MWGPDGKLHDTKA+IPDRCYAGVYQ  I  CK+HGAFDP+TMGSVPNVGLMAQKAEEYG
Sbjct: 364 QMWGPDGKLHDTKALIPDRCYAGVYQETIAFCKEHGAFDPSTMGSVPNVGLMAQKAEEYG 423

Query: 422 SHDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATN 481
           SHDKTF+IPADGVV V D SGK+L+  +VEAGDIWRMCQ KDAPI+DWVKLAV RAR +N
Sbjct: 424 SHDKTFEIPADGVVNVIDASGKVLMSHNVEAGDIWRMCQVKDAPIRDWVKLAVRRARLSN 483

Query: 482 TPAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISV 541
           TPAVFWLD  RAHDAQ+IAKV++YL ++DT GLDI I+SP EATRFSL RI+EGKDTISV
Sbjct: 484 TPAVFWLDANRAHDAQLIAKVKQYLPEHDTDGLDISIMSPEEATRFSLVRIKEGKDTISV 543

Query: 542 TGNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRW 601
           TGNVLRDYLTDLFPI+ELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQ  +EG+LRW
Sbjct: 544 TGNVLRDYLTDLFPILELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQVEKEGHLRW 603

Query: 602 DSLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHF 661
           DSLGEFLALAASLEHL     NPKA VLA TLDQA G+ LD+NKSP+R+VGE+DNRGSHF
Sbjct: 604 DSLGEFLALAASLEHLSQTVGNPKAQVLADTLDQAIGQFLDSNKSPSRRVGELDNRGSHF 663

Query: 662 YLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTD 721
           YLA+YWAQALAAQT+D++LQA F  +A AL+ NE  IV EL  AQG PVD+ GYY  +  
Sbjct: 664 YLAMYWAQALAAQTKDEQLQAHFIPLAHALSANEQVIVAELNNAQGAPVDLGGYYRLDAA 723

Query: 722 LTSKAIRPSATFNAAL 737
              KA+RPS T N  L
Sbjct: 724 KAEKAMRPSETLNKLL 739


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: 1491
Number of extensions: 52
Number of successful extensions: 1
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 7024572 Shewana3_1750 (isocitrate dehydrogenase, NADP-dependent (RefSeq))
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.12916.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 1349.5   1.0          0 1349.4   1.0    1.0  1  lcl|FitnessBrowser__ANA3:7024572  Shewana3_1750 isocitrate dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024572  Shewana3_1750 isocitrate dehydrogenase, NADP-dependent (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1349.4   1.0         0         0       2     739 ..       2     739 ..       1     741 [] 1.00

  Alignments for each domain:
  == domain 1  score: 1349.4 bits;  conditional E-value: 0
                         TIGR00178   2 stekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelaktp 78 
                                         ++++iiyt tdeap+lat sllpi+k+f+++aG++vetrdisl+gr++a+fpe+lt+ qk++d+laelGela+ p
  lcl|FitnessBrowser__ANA3:7024572   2 KDNSPTIIYTETDEAPALATLSLLPIIKTFTDAAGVAVETRDISLSGRVIANFPEKLTDAQKIGDHLAELGELANQP 78 
                                       56789************************************************************************ PP

                         TIGR00178  79 eaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrraplavke 155
                                       eaniiklpnisas+pqlka+i elq+kGyd+p+yp+epktdeek+ikary+kikGsavnpvlreGnsdrrapl+vk+
  lcl|FitnessBrowser__ANA3:7024572  79 EANIIKLPNISASIPQLKACILELQQKGYDIPNYPDEPKTDEEKSIKARYDKIKGSAVNPVLREGNSDRRAPLSVKN 155
                                       ***************************************************************************** PP

                         TIGR00178 156 yarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgevidssvlskk 232
                                       +a+k+ph+mG+w+++s+shvahm++gdfy+se+sv+l +a+ v+i l  kdG+e+vlk+ lkll+ge+id+sv+skk
  lcl|FitnessBrowser__ANA3:7024572 156 FAKKNPHSMGKWTKESQSHVAHMSEGDFYGSEQSVTLANADTVNIVLSQKDGQEVVLKSGLKLLAGEIIDASVMSKK 232
                                       ***************************************************************************** PP

                         TIGR00178 233 alvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlyakiesl 309
                                       alv f+e ei++ak+e+vllslhlkatmmkvsdpi+fGh+v+vf+k vf kha l+ +lG+dv+nG++d+yaki+sl
  lcl|FitnessBrowser__ANA3:7024572 233 ALVSFFEREIANAKAENVLLSLHLKATMMKVSDPIMFGHAVKVFFKPVFDKHASLFAELGVDVNNGFGDVYAKIASL 309
                                       ***************************************************************************** PP

                         TIGR00178 310 paakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyag 386
                                       pa  + +iead+ +vy+erp lamvdsdkGitnlhvpsd+i+dasmpa+ir+sG+m+g+dgkl+dtka+ipd++yag
  lcl|FitnessBrowser__ANA3:7024572 310 PADVRAQIEADIAAVYAERPALAMVDSDKGITNLHVPSDIIIDASMPAAIRSSGQMWGPDGKLHDTKALIPDRCYAG 386
                                       ***************************************************************************** PP

                         TIGR00178 387 vyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqv 463
                                       vyq+ i +ck++Gafdp+tmG+vpnvGlmaqkaeeyGshdktfei+adGvv+v+d+sG+vl+ ++veagdiwrmcqv
  lcl|FitnessBrowser__ANA3:7024572 387 VYQETIAFCKEHGAFDPSTMGSVPNVGLMAQKAEEYGSHDKTFEIPADGVVNVIDASGKVLMSHNVEAGDIWRMCQV 463
                                       ***************************************************************************** PP

                         TIGR00178 464 kdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedt 540
                                       kdapi+dwvklav rarls+tpavfwld +rahd++li+kv++yl +hdt+Gldi i+sp +atrfsl ri++G+dt
  lcl|FitnessBrowser__ANA3:7024572 464 KDAPIRDWVKLAVRRARLSNTPAVFWLDANRAHDAQLIAKVKQYLPEHDTDGLDISIMSPEEATRFSLVRIKEGKDT 540
                                       ***************************************************************************** PP

                         TIGR00178 541 isvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaasle 617
                                       isvtGnvlrdyltdlfpilelGtsakmls+vplm+GGGlfetGaGGsapkhvqq+e+e+hlrwdslGeflalaasle
  lcl|FitnessBrowser__ANA3:7024572 541 ISVTGNVLRDYLTDLFPILELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQVEKEGHLRWDSLGEFLALAASLE 617
                                       ***************************************************************************** PP

                         TIGR00178 618 hvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaealt 694
                                       h++++ gn+ka+vladtld+a+g++ld++kspsr+vGeldnrgs+fyla+ywaq+laaqt+d++l+a+f ++a+al+
  lcl|FitnessBrowser__ANA3:7024572 618 HLSQTVGNPKAQVLADTLDQAIGQFLDSNKSPSRRVGELDNRGSHFYLAMYWAQALAAQTKDEQLQAHFIPLAHALS 694
                                       ***************************************************************************** PP

                         TIGR00178 695 kneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnail 739
                                        ne++ivael+++qG +vdlgGyy  d  +++k++rps+t+n++l
  lcl|FitnessBrowser__ANA3:7024572 695 ANEQVIVAELNNAQGAPVDLGGYYRLDAAKAEKAMRPSETLNKLL 739
                                       ******************************************987 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: 00:00:00.05
# Mc/sec: 9.86
//
[ok]

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

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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