GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Rhodospirillum rubrum ATCC 11170

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_011387859.1 RRU_RS00495 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::Q5H4T8
         (397 letters)



>NCBI__GCF_000013085.1:WP_011387859.1
          Length = 403

 Score =  254 bits (650), Expect = 2e-72
 Identities = 159/395 (40%), Positives = 219/395 (55%), Gaps = 18/395 (4%)

Query: 15  LSLATLAIHGGQSPDPSTGAVMPPIYATSTY---------AQSSPGEHQGFEYSRTHNPT 65
           L+ ATLA+H G + +     V+ P+   +++         + +   E   F Y+R +NPT
Sbjct: 9   LAQATLALHAGTTDESDGAQVLNPLVPATSFFTKPEAVGFSANDMAEDTPFLYTRWNNPT 68

Query: 66  RFAYERCVAALEGGTRAFAFASGMAATSTV-MELLDAGSHVVAMDDLYGGTFRLFERVRR 124
               E  +AALEGG  A  FASGMAA S + +  L AG H+V     Y G   +   +  
Sbjct: 69  NALLEERLAALEGGEAAVVFASGMAALSGLFLSQLKAGDHLVISSVCYAGLAEVAHDILP 128

Query: 125 RTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVV 184
              G+  + VD ++  A +AA+R +T+++ IETP NP+L+L DI A+A IA  HG L  V
Sbjct: 129 GL-GIATTAVDTSNLEAVRAALRPETRLIHIETPGNPILRLSDIEALAAIAHAHGALLSV 187

Query: 185 DNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGG 244
           D+T A+P+  RPL+LGAD V HS TKY  GH D +GG A++G    +A          GG
Sbjct: 188 DSTMATPIATRPLALGADFVAHSLTKYACGHGDALGG-AIIGKAQAMAALRKHALIHFGG 246

Query: 245 VQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKR 304
              PF ++L LRGL+TL LRM  H   A A+A +LE HP + +V++PGL SHPQH LA R
Sbjct: 247 AISPFAAWLILRGLETLSLRMAGHQAGAAAVAAYLEGHPRLRRVLWPGLPSHPQHALACR 306

Query: 305 QMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNH------PAVMTHASI 358
           QM  F G+VS     G   A++  E+ ++ + A SLG   SL+ +       A   H   
Sbjct: 307 QMKNFSGMVSFSADDGPALARQLAERLQVISYAVSLGKTRSLLFYIPTEALIASSFHLDG 366

Query: 359 PVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393
             AR  +    D   RLSVG+ED  DL  DLERAL
Sbjct: 367 DDARSYRDWTGDGTFRLSVGLEDPADLIADLERAL 401


Lambda     K      H
   0.320    0.134    0.391 

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: 449
Number of extensions: 26
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: 397
Length of database: 403
Length adjustment: 31
Effective length of query: 366
Effective length of database: 372
Effective search space:   136152
Effective search space used:   136152
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: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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