GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Shewanella amazonensis SB2B

Align fused aspartate kinase/homoserine dehydrogenase 1 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 6936718 Sama_0905 bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq)

Query= ecocyc::ASPKINIHOMOSERDEHYDROGI-MONOMER
         (820 letters)



>FitnessBrowser__SB2B:6936718
          Length = 821

 Score =  886 bits (2290), Expect = 0.0
 Identities = 464/820 (56%), Positives = 577/820 (70%), Gaps = 9/820 (1%)

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

Query: 61  LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHV----LHGISLLGQCPD 116
              +     +F  L       Q    + Q +  +    +  KH     L G++LLG+CPD
Sbjct: 61  QAVLGRVVGVFEALFDDACQHQ----VPQCREHLFAALSAQKHAWQTRLEGVALLGECPD 116

Query: 117 SINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAA 176
            + A ++  GE++S  +M  ++ A   +   +DP    LA G  LES VDI  S  R   
Sbjct: 117 GVRAEIVVAGERLSTELMVALMNAHWLSADKLDPRALFLAHGTPLESVVDIGVSKPRFKQ 176

Query: 177 SRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCD 236
             + +  + +M GFTA ++KG  V LGRNGSDYSAAVLAACL A  CEIWTDVDGVY  D
Sbjct: 177 LPLDSKRVWVMPGFTAADDKGRTVTLGRNGSDYSAAVLAACLDASSCEIWTDVDGVYNTD 236

Query: 237 PRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIG 296
           PR V DA+LL  +SYQEAMELSYFGAKVLHP+TI PIAQF IPC IKN+ NP+APGTL+ 
Sbjct: 237 PRVVADAKLLSQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPEAPGTLVS 296

Query: 297 ASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEY 356
            + DE  L VK IS+L+N  MF VSGPGMKGMVGMA+R   A++RA +SV LITQSS EY
Sbjct: 297 NAVDETGLQVKAISSLDNQTMFDVSGPGMKGMVGMASRTLGAIARAGVSVSLITQSSCEY 356

Query: 357 SISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKF 416
           SISFCV   D  + + A+++EF LELK  LLEPL +   LAI+S++GDGMRT +G++AKF
Sbjct: 357 SISFCVAGKDAAKVQSALEQEFELELKSELLEPLEMQSGLAIVSLIGDGMRTHKGVAAKF 416

Query: 417 FAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGV 476
           F+ALA+A++NI AIAQGSSERSIS VV        +   HQ  F+  Q ++VF++G G V
Sbjct: 417 FSALAQASVNIRAIAQGSSERSISAVVEQRKVQNAIGACHQRFFDVQQYLDVFLVGAGNV 476

Query: 477 GGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGR 536
           G  LL Q+K Q   LK +HI +RVCG+ANS+ +L +  G++L NWQ  L  ++   +LG 
Sbjct: 477 GAGLLAQVKNQAEALKEQHISIRVCGIANSRKMLLDERGIDLANWQGLLNDSETGCDLGA 536

Query: 537 LIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAA 596
           ++   KE  LLNPV+VDCTSS AVAD+Y + +  G HVVTPNKKANT  + YY  LR AA
Sbjct: 537 MLAWAKEKQLLNPVLVDCTSSAAVADRYLEVMEAGMHVVTPNKKANTRDLGYYRALREAA 596

Query: 597 EKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEA 656
            + RR+FLY+TNVGAGLPVI+NL+ LL AGD+L KF+GILSGSLS+IFGKL+EGMS SEA
Sbjct: 597 LRHRRQFLYETNVGAGLPVIDNLKKLLCAGDKLHKFNGILSGSLSFIFGKLEEGMSLSEA 656

Query: 657 TTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVA 716
           T++AR+  +TEPDPRDDLSGMDVARK+LILARE G  LEL D+ ++ VLPA F+A GDV+
Sbjct: 657 TSIARDKCFTEPDPRDDLSGMDVARKVLILAREVGMPLELEDVVVDSVLPASFDANGDVS 716

Query: 717 AFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGEN 776
            FMANL + D   A  V  AR EGKVLRYVG IDE G CRV I  V    PLF VK GEN
Sbjct: 717 TFMANLHKADTEIATMVENARSEGKVLRYVGQIDESG-CRVSIQAVGPEAPLFSVKGGEN 775

Query: 777 ALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSW 816
           ALAFYS YYQP+P VLRGYGAG DVTAAG FADLLRTL+W
Sbjct: 776 ALAFYSRYYQPIPFVLRGYGAGTDVTAAGAFADLLRTLNW 815


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: 1502
Number of extensions: 47
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: 821
Length adjustment: 42
Effective length of query: 778
Effective length of database: 779
Effective search space:   606062
Effective search space used:   606062
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 Aug 03 2021. The underlying query database was built on Aug 03 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:

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:

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:

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:

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