GapMind for Amino acid biosynthesis

 

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

Align fused aspartate kinase/homoserine dehydrogenase 1 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 7023927 Shewana3_1139 bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq)

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



>FitnessBrowser__ANA3:7023927
          Length = 822

 Score =  919 bits (2374), Expect = 0.0
 Identities = 476/821 (57%), Positives = 595/821 (72%), Gaps = 10/821 (1%)

Query: 1   MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
           M+V+KFGGTS+AN +RF   ADI+   A+   VATVLSAPA +TN L+ M++  + G+D 
Sbjct: 1   MKVMKFGGTSLANWQRFSMAADIVAKAAKAEPVATVLSAPATVTNALLEMVDVAVKGEDY 60

Query: 61  LPNISDAERIFAELL-----TGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCP 115
            P I   ER+F  L      +GL+++Q     A L      + A+ +  L GI+LL +CP
Sbjct: 61  SPVIQHVERVFTSLYQDAVSSGLSSSQSEVLFAGLSV----QLARWQDRLRGITLLQECP 116

Query: 116 DSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIA 175
           D + A ++  GE++S A+M  V+ A+G     +DP E  L  G  LES VDIA S  R  
Sbjct: 117 DGVRAEIVVAGERLSAALMEQVMLAKGITSAQLDPRELFLGRGRPLESVVDIAVSKPRFK 176

Query: 176 ASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTC 235
              +    + +M GFTA +E G++V LGRNGSDYSAAVLAACL A  CEIWTDVDGVY  
Sbjct: 177 NLALDEKRVWVMPGFTAADEDGKVVTLGRNGSDYSAAVLAACLDASSCEIWTDVDGVYNT 236

Query: 236 DPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLI 295
           DPR V DA+LL  +SYQEAMELSYFGAKVLHP+TI PIAQF IPC IKN+ NP APGTL+
Sbjct: 237 DPRVVTDAKLLSQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPDAPGTLV 296

Query: 296 GASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSE 355
               DE  L VK ISNL+N  MF VSGPGMKGMVGMA+R  AA+SR+ +SV LITQSS E
Sbjct: 297 SNQADESGLQVKAISNLDNQTMFDVSGPGMKGMVGMASRTLAAISRSGVSVSLITQSSCE 356

Query: 356 YSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAK 415
           YSISFCV  SD  + + A+++EF LE+K  LLEP+ +   LAI+S++GDGMRT +G++A+
Sbjct: 357 YSISFCVATSDAAKVKSALEQEFELEIKSDLLEPIEMRHDLAIVSLIGDGMRTHKGVAAR 416

Query: 416 FFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGG 475
           FF ALA+A++NI+AIAQGSSERSIS V+        V   HQ  F+  Q ++VF++G G 
Sbjct: 417 FFQALAQASVNIIAIAQGSSERSISTVIEQRKTKHAVAACHQGFFDVQQYLDVFLVGCGN 476

Query: 476 VGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLG 535
           VG  LLEQ+K Q S LK +HI +RVCG+ NS  +L +  G++L NWQ  LA +++P +L 
Sbjct: 477 VGAGLLEQIKHQASVLKEQHISIRVCGIVNSSKMLLDSAGIDLNNWQNLLADSQQPSDLS 536

Query: 536 RLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYA 595
            L+  VKE  LLNPV+VDCTSS  V++QY + +  G HVVTPNKKANT    YY  LR  
Sbjct: 537 ALLAWVKEQQLLNPVLVDCTSSDQVSNQYLEVMNAGMHVVTPNKKANTRDYAYYQALRQT 596

Query: 596 AEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSE 655
           A K RR+FLY+TNVGAGLPVI+NL+ LL AGD+L KF+GILSGSLS+IFGKLDEGM+ SE
Sbjct: 597 ALKQRRQFLYETNVGAGLPVIDNLKKLLFAGDKLHKFNGILSGSLSFIFGKLDEGMTLSE 656

Query: 656 ATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDV 715
           AT LARE  +TEPDPRDDLSGMDVARK+LILARE G +LEL+DI ++ VLP +F+  GDV
Sbjct: 657 ATKLAREKCFTEPDPRDDLSGMDVARKVLILAREVGLKLELSDIVVDSVLPDDFDDSGDV 716

Query: 716 AAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGE 775
            +FMA L++ D   AARVA+A+ +GKVLRYVG I E+G C V+I EVD  DPL+ VK GE
Sbjct: 717 ESFMARLTEADAAIAARVAEAKAQGKVLRYVGQI-EEGACYVRITEVDATDPLYSVKGGE 775

Query: 776 NALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSW 816
           NALAFYS YYQP+P VLRGYGAG +VTAAG FAD+LRTL+W
Sbjct: 776 NALAFYSRYYQPIPFVLRGYGAGTEVTAAGAFADVLRTLNW 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: 1487
Number of extensions: 53
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 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