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

GapMind for Amino acid biosynthesis

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

Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 5208568 Shew_1079 bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq)

Query= BRENDA::P00561
         (820 letters)



>FitnessBrowser__PV4:5208568
          Length = 822

 Score =  913 bits (2359), Expect = 0.0
 Identities = 469/818 (57%), Positives = 596/818 (72%), Gaps = 4/818 (0%)

Query: 1   MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
           M+V+KFGGTS+AN +RF   A I+ ++A +   A VLSAPA +TN L+ M++  ++G D 
Sbjct: 1   MKVMKFGGTSLANWQRFNSAAQIVLASAAEQPTAVVLSAPATVTNGLLEMVDLAVAGDDF 60

Query: 61  LPNISDAERIFAELLTGLAAAQ--PGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSI 118
            P +S    +F + L G AA++   G     L+  +  +    +  L G+ LLG+CPD++
Sbjct: 61  FPVLSQVHEVF-KTLYGQAASEVLSGEQSDSLEAVLAAQLKHWQDKLQGVVLLGECPDAV 119

Query: 119 NAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASR 178
            A ++  GE++S A+M  ++ A G +   + P +  +A G  LES VDIA S +R A   
Sbjct: 120 RAEIVVGGERLSAALMEQLMLAAGVSANQLVPQQLFVAHGPALESVVDIAASKQRFAELS 179

Query: 179 IPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPR 238
           + A  + +M GFTAG++ G +V LGRNGSDYSAAVL+AC+ A CCEIWTDVDGVY  DPR
Sbjct: 180 LDAHQVWVMPGFTAGDKDGRVVTLGRNGSDYSAAVLSACIDASCCEIWTDVDGVYNTDPR 239

Query: 239 QVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGAS 298
            V DA+LL  +SYQEAMELSYFGAKVLHP+TI PIAQ+ IPC I+N+ NPQAPGTL+   
Sbjct: 240 VVADAKLLTQLSYQEAMELSYFGAKVLHPKTIAPIAQYHIPCYIRNSFNPQAPGTLVSNQ 299

Query: 299 RDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSI 358
            DE  L VK ISNL+   MF ++GPGMKGMVGMA+R   A+SR+ +SV LITQSSSEYSI
Sbjct: 300 VDETGLNVKAISNLDEQTMFDIAGPGMKGMVGMASRTLGAISRSGVSVSLITQSSSEYSI 359

Query: 359 SFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFA 418
           SFCV   D  R   A+++EF LELK  +LE +A+   LAI+S++GDGMRT +G++ KFF 
Sbjct: 360 SFCVATQDAERVRVALEQEFELELKSEILEQIAMRHNLAIVSLIGDGMRTHKGVAGKFFQ 419

Query: 419 ALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGG 478
           ALA+AN+NIVAIAQGSSERSIS V+        +   HQ LF+    ++VF++G G VG 
Sbjct: 420 ALAQANVNIVAIAQGSSERSISAVIELRKTKHAIAACHQSLFDVQHYLDVFLVGCGNVGA 479

Query: 479 ALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLI 538
            LLEQ+K+Q   LK +HI +RVCGVANS+ +L +  G++L +WQ  LA +++  +L +++
Sbjct: 480 GLLEQIKQQTEMLKAQHITVRVCGVANSRHMLLDAKGIDLNHWQGLLADSQQACDLDKML 539

Query: 539 RLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEK 598
              K+  LLNPV+VDCTS++AV+DQY   +  G HVVTPNKKANT   DYY  LR  A  
Sbjct: 540 AWAKDQQLLNPVLVDCTSNEAVSDQYVAVMNAGLHVVTPNKKANTRDYDYYRALRQTALH 599

Query: 599 SRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATT 658
            RR+FLY+T VGAGLPVI+NL+ LL AGD+L KF+GILSGSLSYIFG LDEGMS SEAT 
Sbjct: 600 QRRQFLYETTVGAGLPVIDNLKKLLFAGDKLQKFNGILSGSLSYIFGMLDEGMSLSEATG 659

Query: 659 LAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAF 718
           +ARE  +TEPDPRDDLSGMDVARK+LILARE G ++EL+DI++E VLP+ F+A GDV  F
Sbjct: 660 IAREKCFTEPDPRDDLSGMDVARKVLILAREVGMQIELSDIQVESVLPSHFDASGDVETF 719

Query: 719 MANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENAL 778
           MANLS LD   A RV  A+  GKVLRYVG IDE+G CRVKIAEVD  DPL+ VK GENAL
Sbjct: 720 MANLSALDGELAERVNSAKAAGKVLRYVGQIDEEG-CRVKIAEVDAKDPLYSVKGGENAL 778

Query: 779 AFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSW 816
           AFYS YYQP+P VLRGYGAG +VTAAGVFADLLRTL+W
Sbjct: 779 AFYSRYYQPIPFVLRGYGAGTEVTAAGVFADLLRTLNW 816


Lambda     K      H
   0.319    0.135    0.384 

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: 1515
Number of extensions: 40
Number of successful extensions: 5
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: 820
Length of database: 822
Length adjustment: 42
Effective length of query: 778
Effective length of database: 780
Effective search space:   606840
Effective search space used:   606840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Rules (tab-delimited)
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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis