Alignments for a candidate for icd in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Shewanella oneidensis MR-1

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate 201768 SO2629 isocitrate dehydrogenase, NADP-dependent (NCBI ptt file)

Query= SwissProt::P16100
         (741 letters)



>FitnessBrowser__MR1:201768
          Length = 741

 Score = 1069 bits (2764), Expect = 0.0
 Identities = 534/736 (72%), Positives = 609/736 (82%)

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

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

Query: 122 VKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDF 181
           +KARYDKIKGSAVNPVLREGNSDRRAPLSVKN+A+K+PH MG W  DSKSHVAHM  GDF
Sbjct: 124 IKARYDKIKGSAVNPVLREGNSDRRAPLSVKNFAKKNPHSMGKWVKDSKSHVAHMSEGDF 183

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

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

Query: 302 ARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSG 361
           A+I +LP   + +IEADI AVYA+ P LAMV+SDKGITNLHVPSD+I+DASMPA IR SG
Sbjct: 304 AKIASLPTDVRSQIEADIAAVYAEGPALAMVDSDKGITNLHVPSDIIIDASMPAAIRSSG 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+I KV++YL ++DTSGLDI I+SP EATRFSLARI+EGKDTISV
Sbjct: 484 TPAVFWLDANRAHDAQLIVKVKQYLPEHDTSGLDISIMSPEEATRFSLARIKEGKDTISV 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+YWAQALA QT+D++LQA F  +A AL+ NE  IV EL  AQG PVD+ GYY  +  
Sbjct: 664 YLAMYWAQALAVQTKDEQLQAHFIPLAHALSANEQVIVAELNNAQGAPVDLGGYYRLDAV 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: 1512
Number of extensions: 60
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 201768 SO2629 (isocitrate dehydrogenase, NADP-dependent (NCBI ptt file))
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.4851.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 1340.8   1.1          0 1340.6   1.1    1.0  1  lcl|FitnessBrowser__MR1:201768  SO2629 isocitrate dehydrogenase,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201768  SO2629 isocitrate dehydrogenase, NADP-dependent (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1340.6   1.1         0         0       2     739 ..       2     739 ..       1     741 [] 1.00

  Alignments for each domain:
  == domain 1  score: 1340.6 bits;  conditional E-value: 0
                       TIGR00178   2 stekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelaktpea 80 
                                       ++++iiyt tdeap+lat sllpi+k+f+++a ++vetrdisl+gr++a+fpe+lt+ qk++d+laelG+la+ pea
  lcl|FitnessBrowser__MR1:201768   2 KDNSPTIIYTETDEAPALATLSLLPIIKTFTNAADVAVETRDISLSGRVIANFPEKLTDAQKIGDHLAELGDLANQPEA 80 
                                     56789************************************************************************** PP

                       TIGR00178  81 niiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrraplavkeyark 159
                                     niiklpnisas+pqlka+i elq+kGyd+p+yp+epktdeek+ikary+kikGsavnpvlreGnsdrrapl+vk++a+k
  lcl|FitnessBrowser__MR1:201768  81 NIIKLPNISASIPQLKACILELQQKGYDIPNYPDEPKTDEEKSIKARYDKIKGSAVNPVLREGNSDRRAPLSVKNFAKK 159
                                     ******************************************************************************* PP

                       TIGR00178 160 hphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgevidssvlskkalvefl 238
                                     +ph+mG+w +dskshvahm++gdfy+se sv+l +a+ v+i l  kdG+e+vlk+ lkll+ge+id+sv+skkalv f+
  lcl|FitnessBrowser__MR1:201768 160 NPHSMGKWVKDSKSHVAHMSEGDFYGSELSVTLSNADTVNIVLAQKDGQEVVLKSGLKLLAGEIIDASVMSKKALVSFF 238
                                     ******************************************************************************* PP

                       TIGR00178 239 eeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlyakieslpaakkeei 317
                                     e ei++ak+e+vllslhlkatmmkvsdpi+fGh+v+vf+k vf kha+l+ +lG+dv+nG++d+yaki+slp   + +i
  lcl|FitnessBrowser__MR1:201768 239 EREIANAKAENVLLSLHLKATMMKVSDPIMFGHAVKVFFKPVFDKHAALFAELGVDVNNGFGDVYAKIASLPTDVRSQI 317
                                     ******************************************************************************* PP

                       TIGR00178 318 eadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedck 396
                                     ead+ +vy+e+p lamvdsdkGitnlhvpsd+i+dasmpa+ir+sG+m+g+dgkl+dtka+ipd++yagvyq+ i +ck
  lcl|FitnessBrowser__MR1:201768 318 EADIAAVYAEGPALAMVDSDKGITNLHVPSDIIIDASMPAAIRSSGQMWGPDGKLHDTKALIPDRCYAGVYQETIAFCK 396
                                     ******************************************************************************* PP

                       TIGR00178 397 knGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqvkdapiqdwvkla 475
                                     ++Gafdp+tmG+vpnvGlmaqkaeeyGshdktfei+adGvv+v+d+sG+vl+ ++veagdiwrmcqvkdapi+dwvkla
  lcl|FitnessBrowser__MR1:201768 397 EHGAFDPSTMGSVPNVGLMAQKAEEYGSHDKTFEIPADGVVNVIDASGKVLMSHNVEAGDIWRMCQVKDAPIRDWVKLA 475
                                     ******************************************************************************* PP

                       TIGR00178 476 vtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltd 554
                                     v rarls+tpavfwld +rahd++li kv++yl +hdt+Gldi i+sp +atrfsl+ri++G+dtisvtGnvlrdyltd
  lcl|FitnessBrowser__MR1:201768 476 VRRARLSNTPAVFWLDANRAHDAQLIVKVKQYLPEHDTSGLDISIMSPEEATRFSLARIKEGKDTISVTGNVLRDYLTD 554
                                     ******************************************************************************* PP

                       TIGR00178 555 lfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaaslehvavktgnekakvlad 633
                                     lfpilelGtsakmls+vplm+GGGlfetGaGGsapkhvqq+e+e+hlrwdslGeflalaasleh++++ gn+ka+vlad
  lcl|FitnessBrowser__MR1:201768 555 LFPILELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQVEKEGHLRWDSLGEFLALAASLEHLSQTVGNPKAQVLAD 633
                                     ******************************************************************************* PP

                       TIGR00178 634 tldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeav 712
                                     tld+a+g++ld++kspsr+vGeldnrgs+fyla+ywaq+la qt+d++l+a+f ++a+al+ ne++ivael+++qG +v
  lcl|FitnessBrowser__MR1:201768 634 TLDQAIGQFLDSNKSPSRRVGELDNRGSHFYLAMYWAQALAVQTKDEQLQAHFIPLAHALSANEQVIVAELNNAQGAPV 712
                                     ******************************************************************************* PP

                       TIGR00178 713 dlgGyyapdtdlttkvlrpsatfnail 739
                                     dlgGyy  d  +++k++rps+t+n++l
  lcl|FitnessBrowser__MR1:201768 713 DLGGYYRLDAVKAEKAMRPSETLNKLL 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 8.48
//
[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