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_011388544.1 RRU_RS04120 PLP-dependent aspartate aminotransferase family protein

Query= BRENDA::Q5H4T8
         (397 letters)



>NCBI__GCF_000013085.1:WP_011388544.1
          Length = 390

 Score =  465 bits (1197), Expect = e-136
 Identities = 230/376 (61%), Positives = 290/376 (77%), Gaps = 1/376 (0%)

Query: 18  ATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALE 77
           AT A+H G   D +TGAVM PIYATST+AQSSPG+H G+EY+R+ NPTR A+ER VA LE
Sbjct: 13  ATWAVHAGHGADATTGAVMTPIYATSTFAQSSPGKHTGWEYARSGNPTRAAFERAVAELE 72

Query: 78  GGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLT 137
           GGT  +AFASG+AA +T+++LLD G+H++A DDLYGG++RLFE+VR R+AGL  S+VD +
Sbjct: 73  GGTNGYAFASGLAAEATILDLLDHGAHIIAGDDLYGGSWRLFEKVRARSAGLTVSYVDPS 132

Query: 138 DPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPL 197
           D  A   AI   TK++WIETP+NP+LK+ D+AA+A +A++HGL TVVD+TFA+P +QRPL
Sbjct: 133 DLGAVAQAITPQTKLIWIETPSNPLLKIADLAALAALAKEHGLRTVVDSTFATPWIQRPL 192

Query: 198 SLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRG 257
            LG D+VVHSATKYLNGHSD++ G+ VV D  +LA Q+ FLQN+ G V  PF +FLALRG
Sbjct: 193 DLGIDIVVHSATKYLNGHSDVIAGVVVVKD-PDLASQLGFLQNATGAVLDPFAAFLALRG 251

Query: 258 LKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVL 317
           LKTL LRM  H  N LA+A  LE    + +V+YPGLASHPQH LA++QM  FGG++++ L
Sbjct: 252 LKTLALRMDRHSANGLAVAHALEGRAKVRRVLYPGLASHPQHALARQQMRAFGGMLTLDL 311

Query: 318 KGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSV 377
           +       RF E  +LFTLAESLGGVESL  HP  M+H SIPV RR  LGI+D LVRLSV
Sbjct: 312 ESDLAGTVRFLEALKLFTLAESLGGVESLAGHPVTMSHGSIPVERRTALGITDTLVRLSV 371

Query: 378 GIEDLGDLRGDLERAL 393
           GIED GDL  DL++AL
Sbjct: 372 GIEDAGDLIADLDQAL 387


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: 521
Number of extensions: 23
Number of successful extensions: 2
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: 390
Length adjustment: 31
Effective length of query: 366
Effective length of database: 359
Effective search space:   131394
Effective search space used:   131394
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