Alignments for a candidate for icd in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Shewanella loihica PV-4

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate 5209085 Shew_1563 isocitrate dehydrogenase, NADP-dependent (RefSeq)

Query= BRENDA::Q1XIQ9
         (743 letters)



>FitnessBrowser__PV4:5209085
          Length = 739

 Score = 1086 bits (2808), Expect = 0.0
 Identities = 534/736 (72%), Positives = 613/736 (83%)

Query: 4   DNSKIIYTITDEAPALATYSLLPIIQAYTASSGINVETRDISLAGRVLANFPKYLTKEQR 63
           DN  IIYT TDEAPALAT SLLPII+ +TA++G+ VETRDISL+GRV+ANFP++L  EQ+
Sbjct: 3   DNPTIIYTETDEAPALATLSLLPIIKHFTAAAGVGVETRDISLSGRVIANFPEFLKPEQQ 62

Query: 64  IDDALAELGEMVTNPNANIIKLPNISASVPQLHAVIKELQGKGYEVPNYPEEPQNDAEKS 123
           I DALAELGE+ T P ANIIKLPNISAS+PQL A IKELQ K Y +PNYP+EPQNDAE  
Sbjct: 63  ISDALAELGELATKPEANIIKLPNISASIPQLKACIKELQDKDYALPNYPDEPQNDAEAD 122

Query: 124 IKYTYDKIKGSAVNPVLREGNSDRRAPASVKQYAQKNPHSMGVWSSESKSHVASMSGGDF 183
           IK  YDKIKGSAVNPVLREGNSDRRAP SVK YA+KNPHSMG WSS+SKSHVA M  GDF
Sbjct: 123 IKARYDKIKGSAVNPVLREGNSDRRAPTSVKNYAKKNPHSMGAWSSDSKSHVAHMEAGDF 182

Query: 184 YESEQSATVNYATNVKIEFVGQDGSVKVLKDSLPLLTGEIIDSSVLSKVSLLEFYQQSIT 243
           Y SEQS TV   T++ I F G+DGS K LK  L LL GE+ID+S +SK +L+ F ++ I 
Sbjct: 183 YGSEQSVTVAEPTSIDILFEGKDGSSKTLKAGLKLLAGEVIDASTMSKKALVAFMEREIE 242

Query: 244 DAKKEDVLLSLHLKATMMKVSDPVIFGYAVKVFYADVFEKHGEIFDQLGVDANNGIGDVY 303
            AK EDVLLSLHLKATMMKVSDP++FG+AVKVFY  +FEKHG++F++LGVD NNG GDVY
Sbjct: 243 AAKAEDVLLSLHLKATMMKVSDPIMFGHAVKVFYKSLFEKHGQLFEELGVDVNNGFGDVY 302

Query: 304 SKISRLPSDKQAEIEADLAAVFANRPELAMVDSDKGITNLHVPSDVIVDASMPATLRSSG 363
           +KI+ LP+DK+AEIEAD+AA++  RP LAMVDSD+GITNLHVPSDVI+DASMPA +RSSG
Sbjct: 303 AKIASLPADKKAEIEADIAAIYTERPALAMVDSDRGITNLHVPSDVIIDASMPAAIRSSG 362

Query: 364 RMWGPDGELKDTKAMIPDRCYAGVYQTVFDFCKENGAFDPTTMGTVPNVGLMAQKAEEYG 423
           +MWGPDG+LKDTKA+IPDRCYAGVYQ    FCKENGAFDPTTMG+VPNVGLMAQKAEEYG
Sbjct: 363 QMWGPDGKLKDTKALIPDRCYAGVYQETIQFCKENGAFDPTTMGSVPNVGLMAQKAEEYG 422

Query: 424 SHDKTFIMSEAGSMRVVDALGTTLLEHSVEEGDLWRMCQAKDLPIQDWVKLTITRAKASG 483
           SHDKTF ++  G ++VVDA G  L+ H VE GD+WRMCQ KD PI+DWVKL + RA+ S 
Sbjct: 423 SHDKTFEIAADGVVKVVDAAGNLLMSHDVEAGDIWRMCQVKDAPIRDWVKLAVNRARLSS 482

Query: 484 MPAVFWLDENRAHDREMIKKVNAYLANYDTTGLDIQTLSPVEACKFTLARIIKGEDTISV 543
            PAVFWLDENRAHD ++I KV  YL  +DT GL+I  ++PV A +F+L RI +G DTISV
Sbjct: 483 TPAVFWLDENRAHDAQLIAKVKQYLPEHDTDGLEIHIMAPVAATRFSLERIKQGLDTISV 542

Query: 544 TGNVLRDYLTDLFPILELGTSAKMLSVVPLMNGGGLFETGAGGSAPKHVQQFEKENHLRW 603
           TGNVLRDYLTDLFPILELGTSAKMLS+VPLM+GGGLFETGAGGSAPKHVQQ EKE HLRW
Sbjct: 543 TGNVLRDYLTDLFPILELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQVEKEGHLRW 602

Query: 604 DSLGEFLALAASLEHLSVTSGNAKAQVLADTLDKATGEFLDSNKSPSRRVGELDNRGSHF 663
           DSLGEFLAL ASLEHLS   GN KAQVLAD LD A G+FLD N+SPSRRVGELDNRGSHF
Sbjct: 603 DSLGEFLALGASLEHLSQNYGNPKAQVLADALDNAIGKFLDENRSPSRRVGELDNRGSHF 662

Query: 664 YLAMYWAKALAQQTSDGELKASFTGVAQAFAKKEEKIVAELNAAQGPAMNIGGYYFADTA 723
           YLAMYWA+ALA Q SD ELKA F  +A+A    E KIVAELN AQGPA+++GGYY  D  
Sbjct: 663 YLAMYWAQALAAQDSDAELKAQFAPLAEALTNNEAKIVAELNGAQGPAVDLGGYYRLDAV 722

Query: 724 QAEKAMRPSETLNTIL 739
           +AE AMRPS TLN ++
Sbjct: 723 KAEAAMRPSATLNQLI 738


Lambda     K      H
   0.314    0.131    0.369 

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: 1498
Number of extensions: 49
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: 743
Length of database: 739
Length adjustment: 40
Effective length of query: 703
Effective length of database: 699
Effective search space:   491397
Effective search space used:   491397
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: 42 (22.0 bits)
S2: 55 (25.8 bits)

Align candidate 5209085 Shew_1563 (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.28545.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 1343.8   0.5          0 1343.7   0.5    1.0  1  lcl|FitnessBrowser__PV4:5209085  Shew_1563 isocitrate dehydrogena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209085  Shew_1563 isocitrate dehydrogenase, NADP-dependent (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1343.7   0.5         0         0       4     739 ..       3     738 ..       1     739 [] 1.00

  Alignments for each domain:
  == domain 1  score: 1343.7 bits;  conditional E-value: 0
                        TIGR00178   4 ekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelaktpean 81 
                                      ++++iiyt tdeap+lat sllpi+k f+a+aG+ vetrdisl+gr++a+fpe+l  eq+++dalaelGela+ pean
  lcl|FitnessBrowser__PV4:5209085   3 DNPTIIYTETDEAPALATLSLLPIIKHFTAAAGVGVETRDISLSGRVIANFPEFLKPEQQISDALAELGELATKPEAN 80 
                                      789*************************************************************************** PP

                        TIGR00178  82 iiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrraplavkeyark 159
                                      iiklpnisas+pqlka+ikelqdk y+lp+yp+ep++d+e dikary+kikGsavnpvlreGnsdrrap++vk+ya+k
  lcl|FitnessBrowser__PV4:5209085  81 IIKLPNISASIPQLKACIKELQDKDYALPNYPDEPQNDAEADIKARYDKIKGSAVNPVLREGNSDRRAPTSVKNYAKK 158
                                      ****************************************************************************** PP

                        TIGR00178 160 hphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgevidssvlskkalvef 237
                                      +ph+mG+ws dskshvahm+agdfy+se+sv++ +++++ i +  kdG++  lka lkll+gevid+s +skkalv+f
  lcl|FitnessBrowser__PV4:5209085 159 NPHSMGAWSSDSKSHVAHMEAGDFYGSEQSVTVAEPTSIDILFEGKDGSSKTLKAGLKLLAGEVIDASTMSKKALVAF 236
                                      ****************************************************************************** PP

                        TIGR00178 238 leeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlyakieslpaakke 315
                                      +e eie ak+e+vllslhlkatmmkvsdpi+fGh+v+vfyk  f kh++l+e+lG+dv+nG++d+yaki+slpa kk 
  lcl|FitnessBrowser__PV4:5209085 237 MEREIEAAKAEDVLLSLHLKATMMKVSDPIMFGHAVKVFYKSLFEKHGQLFEELGVDVNNGFGDVYAKIASLPADKKA 314
                                      ****************************************************************************** PP

                        TIGR00178 316 eieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyqavie 393
                                      eiead+ ++y erp lamvdsd+Gitnlhvpsdvi+dasmpa+ir+sG+m+g+dgklkdtka+ipd++yagvyq+ i+
  lcl|FitnessBrowser__PV4:5209085 315 EIEADIAAIYTERPALAMVDSDRGITNLHVPSDVIIDASMPAAIRSSGQMWGPDGKLKDTKALIPDRCYAGVYQETIQ 392
                                      ****************************************************************************** PP

                        TIGR00178 394 dckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqvkdapiqdw 471
                                      +ck+nGafdpttmG+vpnvGlmaqkaeeyGshdktfei adGvv+vvd+ G++l+ ++veagdiwrmcqvkdapi+dw
  lcl|FitnessBrowser__PV4:5209085 393 FCKENGAFDPTTMGSVPNVGLMAQKAEEYGSHDKTFEIAADGVVKVVDAAGNLLMSHDVEAGDIWRMCQVKDAPIRDW 470
                                      ****************************************************************************** PP

                        TIGR00178 472 vklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnvlr 549
                                      vklav+rarls+tpavfwld++rahd++li+kv++yl +hdt+Gl+i+i+ pv atrfsleri++G dtisvtGnvlr
  lcl|FitnessBrowser__PV4:5209085 471 VKLAVNRARLSSTPAVFWLDENRAHDAQLIAKVKQYLPEHDTDGLEIHIMAPVAATRFSLERIKQGLDTISVTGNVLR 548
                                      ****************************************************************************** PP

                        TIGR00178 550 dyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaaslehvavktgnek 627
                                      dyltdlfpilelGtsakmls+vplm+GGGlfetGaGGsapkhvqq+e+e+hlrwdslGeflal+asleh+++++gn+k
  lcl|FitnessBrowser__PV4:5209085 549 DYLTDLFPILELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQVEKEGHLRWDSLGEFLALGASLEHLSQNYGNPK 626
                                      ****************************************************************************** PP

                        TIGR00178 628 akvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaealtkneekivaela 705
                                      a+vlad+ld+a+gk+lde++spsr+vGeldnrgs+fyla+ywaq+laaq  d+el+a+fa++aealt+ne+kivael+
  lcl|FitnessBrowser__PV4:5209085 627 AQVLADALDNAIGKFLDENRSPSRRVGELDNRGSHFYLAMYWAQALAAQDSDAELKAQFAPLAEALTNNEAKIVAELN 704
                                      ****************************************************************************** PP

                        TIGR00178 706 avqGeavdlgGyyapdtdlttkvlrpsatfnail 739
                                       +qG+avdlgGyy  d  ++++++rpsat+n+++
  lcl|FitnessBrowser__PV4:5209085 705 GAQGPAVDLGGYYRLDAVKAEAAMRPSATLNQLI 738
                                      *******************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (739 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 0.01s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 10.04
//
[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