GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Pseudomonas baetica a390

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_016986598.1 C0J26_RS09040 branched-chain amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>NCBI__GCF_003031005.1:WP_016986598.1
          Length = 375

 Score =  542 bits (1397), Expect = e-159
 Identities = 265/372 (71%), Positives = 313/372 (84%)

Query: 1   MKKGTQRLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQI 60
           M K T+++S+LFAAM +AG AS+S AADTIKI +AGP TGPVAQYGDMQ +GA MAIEQI
Sbjct: 1   MTKATKQISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGAKMAIEQI 60

Query: 61  NKAGGVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEG 120
           N  GGV+G +LE V YDDACDPKQAVAVANKVVNDGVKFVVGH+CSSSTQPA+DIYEDEG
Sbjct: 61  NAKGGVDGKKLEAVEYDDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEG 120

Query: 121 VLMITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEG 180
           V+MITP+AT+P+IT+RGYK+IFRTIGLD+ QGP AG +IA+  K K + VLHDKQQYGEG
Sbjct: 121 VIMITPAATSPDITARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVGVLHDKQQYGEG 180

Query: 181 IATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQA 240
           IAT VK T+E  G KVAVFEG+NAGDKDF+A+I+KLK+A V FVY+GGYHPE+GL+LRQA
Sbjct: 181 IATAVKSTLEKKGTKVAVFEGVNAGDKDFSAIIAKLKQANVDFVYYGGYHPELGLILRQA 240

Query: 241 KQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPS 300
           ++ GL A+FMGPEGVGN  IT IA DA+EG+L TLP++F+QDP N AL DAFKAK +DPS
Sbjct: 241 QEKGLKAKFMGPEGVGNDSITQIAKDAAEGLLVTLPKSFDQDPANIALADAFKAKKEDPS 300

Query: 301 GIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTV 360
           G FV P+YSAV VIA+GI+ A   D  KVAEA+ A TF+TPTG+L FD KGDLK+F F V
Sbjct: 301 GPFVFPSYSAVEVIAEGIKAAKSEDATKVAEAIHAGTFKTPTGDLSFDAKGDLKDFKFVV 360

Query: 361 YEWHKDATRTEV 372
           YEWH    +TEV
Sbjct: 361 YEWHNGKPKTEV 372


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: 563
Number of extensions: 18
Number of successful extensions: 1
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: 375
Length adjustment: 30
Effective length of query: 343
Effective length of database: 345
Effective search space:   118335
Effective search space used:   118335
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 24 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