GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Herbaspirillum seropedicae SmR1

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate HSERO_RS08270 HSERO_RS08270 amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__HerbieS:HSERO_RS08270
          Length = 373

 Score =  462 bits (1190), Expect = e-135
 Identities = 225/374 (60%), Positives = 292/374 (78%), Gaps = 5/374 (1%)

Query: 3   KGTQRLSRLFAAMAIAGFASYSMAA--DTIKIALAGPVTGPVAQYGDMQRAGALMAIEQI 60
           K   RL+++  A+A A FA+++  A  +T+KIA+AGP+TG VAQYGDM +AGAL AIEQI
Sbjct: 2   KFASRLTKI--ALAAATFAAFAGVAHAETVKIAIAGPMTGAVAQYGDMVKAGALTAIEQI 59

Query: 61  NKAGGVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEG 120
           N AGG NG + E V+ DDAC+PKQAVAVANK+V+ G+K+V+GHVCS ST PA+DIYE+EG
Sbjct: 60  NAAGGANGNKFEAVMMDDACEPKQAVAVANKIVSQGIKYVIGHVCSGSTIPASDIYENEG 119

Query: 121 VLMITPSATAPEIT-SRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGE 179
           V+MITPSATAP++T ++ +K IFRTIG D+ QGP A +++ E+ K K +AVLHDKQ YG+
Sbjct: 120 VVMITPSATAPQLTEAKPHKFIFRTIGRDDQQGPAAARYVIEKLKPKKVAVLHDKQSYGQ 179

Query: 180 GIATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQ 239
           G+A+ VK  ++ A + V VFEG+NAGD D++A+++KLK  GV FVYFGGYHPEMGL++RQ
Sbjct: 180 GVASSVKAALDAAKVPVVVFEGINAGDSDYSAIVTKLKSQGVDFVYFGGYHPEMGLIMRQ 239

Query: 240 AKQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDP 299
           A++ G+ A FMGPEGVGN +ITAIAG ASEGML TLP  F  DP N AL+ AF A  +DP
Sbjct: 240 AREQGIKAVFMGPEGVGNKDITAIAGPASEGMLVTLPADFAADPANAALVKAFAAAKRDP 299

Query: 300 SGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFT 359
           +G F +PAYS V +IA  I  A   DPEKVA  + AN+F+TP GN+ +D+KGDLK+F F 
Sbjct: 300 NGPFQMPAYSGVKIIADAIAGAKSTDPEKVAAYIHANSFKTPIGNVEYDKKGDLKSFKFV 359

Query: 360 VYEWHKDATRTEVK 373
           V+ WHKDA++TE K
Sbjct: 360 VFTWHKDASKTEAK 373


Lambda     K      H
   0.316    0.133    0.377 

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: 506
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: 373
Length of database: 373
Length adjustment: 30
Effective length of query: 343
Effective length of database: 343
Effective search space:   117649
Effective search space used:   117649
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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