GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08260 in Pseudomonas litoralis 2SM5

Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate WP_090272111.1 BLU11_RS03770 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:G8ALJ3
         (366 letters)



>NCBI__GCF_900105005.1:WP_090272111.1
          Length = 375

 Score =  291 bits (746), Expect = 1e-83
 Identities = 150/357 (42%), Positives = 220/357 (61%), Gaps = 3/357 (0%)

Query: 5   LSLLVAVAATAMTASVAKA--DIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVL 62
           LS  VAV A A  +S+  A   I +A AGP+TG  A +G+    G   A+  IN AGGV 
Sbjct: 9   LSQFVAVTALAGISSLTLAAETIRIALAGPVTGAVAQYGDMQFTGANMAIDMINKAGGVN 68

Query: 63  GQKLKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPA 122
           G +L+  V DDACDPKQAVAVAN++   G+ FV GH CS S+ PA+ +Y +EG+L ++PA
Sbjct: 69  GSQLEGVVFDDACDPKQAVAVANRIVNDGISFVVGHLCSSSTQPATDIYEDEGILMVTPA 128

Query: 123 STNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQK 182
           +T+P +T +  + +FR  G D  QG  AGK+++EN K + VA++HDK  YG+G+A   + 
Sbjct: 129 ATSPDITSRGYELIFRTIGLDSLQGPTAGKFIVENIKPEKVAVIHDKQQYGEGIATAVRG 188

Query: 183 ALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNA 242
            L   G    I++  TAG+KD+SAL+++L+Q  VD VY GGYH E GL+ RQ ++QGLN 
Sbjct: 189 VLTEAGIDVPIFDGITAGDKDFSALIARLRQAQVDFVYFGGYHPELGLILRQAREQGLNV 248

Query: 243 PIVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEG-YTLYT 301
             +  + +  ++  AI G A E  ++T      E P     VE F++   +P G +   +
Sbjct: 249 KFMGPEGVGNSDISAIAGAAAEGMLVTLPKAFDEDPANAPLVEAFKERKQDPRGPFVFPS 308

Query: 302 YAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWN 358
           YAA+Q+ A+  + A STD   +A+ LR N+++T  GK+ FD KGD+    +V Y W+
Sbjct: 309 YAAVQVIADGIRLAESTDPFDVAEALRNNTFDTPTGKLAFDEKGDLKDFNFVVYEWH 365


Lambda     K      H
   0.312    0.129    0.366 

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: 383
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: 366
Length of database: 375
Length adjustment: 30
Effective length of query: 336
Effective length of database: 345
Effective search space:   115920
Effective search space used:   115920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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