GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00885 in Pseudomonas stutzeri RCH2

Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate GFF3786 Psest_3855 Branched-chain amino acid ABC-type transport system, permease components

Query= uniprot:D8IUY4
         (309 letters)



>FitnessBrowser__psRCH2:GFF3786
          Length = 295

 Score =  145 bits (365), Expect = 1e-39
 Identities = 95/302 (31%), Positives = 162/302 (53%), Gaps = 24/302 (7%)

Query: 4   FIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPG 63
           F+ Q++ GL+ GS YA+++LG  +++G+L +INFAHG   M+GA  G  LL  +     G
Sbjct: 12  FLGQLLIGLINGSFYAMLSLGLAIIFGMLKIINFAHGAQYMIGAFAGYLLLATL-----G 66

Query: 64  LPGIVQLVIA--IVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAMM 121
           +     L++A  IVG      + S +IER+A   L N   L  L+   G+++ L+     
Sbjct: 67  IGYWPALILAPIIVG------LCSAVIERLALSRLYNLDHLYSLLFTFGLALALEGAFRY 120

Query: 122 IWGRSPLPFPQVMPSDPVHIAGALISPTQIMLLALAVLAM-VGLVLIVEKTKMGRAMRAT 180
            +G S  P+         +  G +  P     + LA L + +   L++EKTK+G  +RA 
Sbjct: 121 FYGSSGQPYAVPKELAGGYNLGFMFLPKYRAWVVLASLVICIASWLLIEKTKLGAYLRAA 180

Query: 181 AENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAV 240
            ENP +    G++   ++  T+ +GA LA +AG++ A  Y  +   MG    +  F+  V
Sbjct: 181 TENPTLVRTFGINVPLLLTFTYGMGAALAGLAGMLAAPIYQVSPL-MGSNLIIVVFAVVV 239

Query: 241 LGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGI 300
           +GG+G+I GA++ G +LG++E L   +  + +         +I  F+++ IVL +RP+G+
Sbjct: 240 VGGMGSILGAIITGYMLGILEGLTKVFYPEAS---------NIVIFVIMAIVLLVRPAGL 290

Query: 301 MG 302
           MG
Sbjct: 291 MG 292


Lambda     K      H
   0.328    0.144    0.416 

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: 274
Number of extensions: 18
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: 309
Length of database: 295
Length adjustment: 27
Effective length of query: 282
Effective length of database: 268
Effective search space:    75576
Effective search space used:    75576
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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