GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ilvE in Phaeobacter inhibens BS107

Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate GFF3443 PGA1_c34960 putative branched-chain-amino-acid aminotransferase, subunit A

Query= curated2:O29329
         (290 letters)



>FitnessBrowser__Phaeo:GFF3443
          Length = 302

 Score =  185 bits (470), Expect = 9e-52
 Identities = 109/291 (37%), Positives = 165/291 (56%), Gaps = 17/291 (5%)

Query: 2   LYVYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDL 61
           + +Y++GE VP+ EAKVS++D GF+ GDGV+EG+R YNG    + EH+DRL+++AK IDL
Sbjct: 19  ILIYLNGEIVPKAEAKVSVYDSGFMLGDGVWEGLRLYNGTWAFIDEHLDRLFEAAKTIDL 78

Query: 62  EIPITKEEFMEIILETLRKNNLR-DAYIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGK 120
           +I + +++  + +L+T   N++  DA+ R +VTRG+       R  Q+PS+       G 
Sbjct: 79  DIGMDRDQVKQAVLDTQDANDMTSDAHARLMVTRGVKS-----RPFQHPSL----SQQGP 129

Query: 121 LYGDLYEKGLTAITVAVRRNSFDAL-------PPNIKSLNYLNNILAKIEANAKGGDEAI 173
            +  + E     +   +R  +   L        P + S + LN ILA I A   G DE +
Sbjct: 130 TFTIIMEHSRPNLPRPIRLATVPHLRGLPMTQDPKLNSHSKLNCILACIAAEKAGADEGL 189

Query: 174 FLDRNGYVSEGSGDNIFVVKNGAITTPPTINNLRGITREAVIEIINRLGIPFKETNIGLY 233
            LD NG+V+  +  N F+V+ GA+ T      + GITR+ VI++     IP  E N  L 
Sbjct: 190 MLDVNGFVNTTNACNFFIVRKGAVWTSTGDYCMNGITRQKVIDLCRANDIPVFERNYSLV 249

Query: 234 DLYTADEVFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLMEEFSKLTESE 284
           D Y ADE F+TGT     P+  IDGR+IGDG+ G +T++L   +  L   E
Sbjct: 250 DTYGADEAFLTGTFGAQTPVGDIDGRQIGDGEMGPVTKRLRALYKDLIAQE 300


Lambda     K      H
   0.319    0.142    0.409 

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: 266
Number of extensions: 16
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: 290
Length of database: 302
Length adjustment: 26
Effective length of query: 264
Effective length of database: 276
Effective search space:    72864
Effective search space used:    72864
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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