GapMind for Amino acid biosynthesis

 

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

Align cystathionine beta-lyase (EC 4.4.1.8) (characterized)
to candidate 7025253 Shewana3_2414 cystathionine beta-lyase (RefSeq)

Query= BRENDA::P06721
         (395 letters)



>FitnessBrowser__ANA3:7025253
          Length = 399

 Score =  417 bits (1072), Expect = e-121
 Identities = 208/394 (52%), Positives = 279/394 (70%), Gaps = 6/394 (1%)

Query: 1   MADK-KLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRR 59
           M DK +L TQ+V+ GR KK+T G +N  + RAS++VFD++E  +HA +N+ NGE+FYGRR
Sbjct: 1   MTDKHQLATQIVSVGRDKKWTKGVINPPVFRASTIVFDTMEDMRHAAKNKTNGEMFYGRR 60

Query: 60  GTLTHFSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCS 119
           GT THF+ Q A+ ELEGGAG  L+P GAAA++ ++L+F++ GDH+LM ++ YEP++D CS
Sbjct: 61  GTPTHFAFQAAISELEGGAGTALYPSGAAAISAALLSFLQAGDHLLMVDSVYEPTRDLCS 120

Query: 120 KILSKLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPD 179
            IL+   + T+++DPLIG  I + ++PNTK++FLESPGSITMEV DVP +          
Sbjct: 121 HILAGFNIETTYYDPLIGEGIRELIRPNTKVLFLESPGSITMEVQDVPTLCRIAHE--HG 178

Query: 180 AIIMIDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQLRENAYL 239
            + ++DNTWA+ +  K  + G+DVSIQAATKY+VGHSD MIGTA  N + W QLRE +YL
Sbjct: 179 LVTILDNTWASPINSKPFEMGVDVSIQAATKYIVGHSDVMIGTATANEKHWPQLRERSYL 238

Query: 240 MGQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEF 299
           +GQ    D  Y+ +RGLRTLGVR+ QH +++LKVA WL   P+V  + HPA     GHEF
Sbjct: 239 LGQTTSPDDVYLATRGLRTLGVRMAQHEKNALKVANWLKTRPEVDHLRHPAFDTCPGHEF 298

Query: 300 WKRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIR 359
           +KRDF+ ++GLFSFVLK+  + E +   ++N   F M +SWGGYESLIL      I  IR
Sbjct: 299 FKRDFSAANGLFSFVLKQG-DQEAVTALVENMQHFKMGFSWGGYESLILG--IFGIEKIR 355

Query: 360 PQGEIDFSGTLIRLHIGLEDVDDLIADLDAGFAR 393
              + D    LIR+HIGLED DDLIADL AGF R
Sbjct: 356 SATQWDARKPLIRVHIGLEDPDDLIADLSAGFER 389


Lambda     K      H
   0.321    0.135    0.402 

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: 439
Number of extensions: 16
Number of successful extensions: 4
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: 395
Length of database: 399
Length adjustment: 31
Effective length of query: 364
Effective length of database: 368
Effective search space:   133952
Effective search space used:   133952
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 (21.9 bits)
S2: 50 (23.9 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