GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24005 in Pseudomonas putida KT2440

Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate PP_0281 PP_0281 Amino acid ABC transporter, permease protein

Query= uniprot:B2TBJ7
         (240 letters)



>FitnessBrowser__Putida:PP_0281
          Length = 230

 Score =  172 bits (435), Expect = 7e-48
 Identities = 93/232 (40%), Positives = 140/232 (60%), Gaps = 6/232 (2%)

Query: 4   IQMLGFGPEGWGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTT 63
           I + GFGP      ++   LMTV L L AL +G V G L A AK S F+ L+ +G  Y+T
Sbjct: 3   IDLHGFGP-----AMMAGTLMTVKLALCALLLGLVLGLLGALAKTSPFKPLQWLGGFYST 57

Query: 64  VFRGVPELLVIYLFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYR 123
           + RGVPELL + L YFG   L+ S+G+     G + +  F  G +A+G+  GAY  EV+R
Sbjct: 58  LVRGVPELLWVLLIYFGTVGLMNSLGEALNMPG-LELSAFAAGVIALGLCFGAYATEVFR 116

Query: 124 SAVLAVSRGELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGL 183
            A+LA+ +G  EA  ++G+    +  RI++PQ+ R ALPG+GN++ + +KD+AL+SV GL
Sbjct: 117 GAILAIPKGHREAGLALGLSKGRILSRIILPQMWRIALPGLGNLFMILMKDTALVSVIGL 176

Query: 184 AELLRTSQVAAGSTHQYFTFFVVGGALYLIMTSISNRVFNRAEAHVGRSFKR 235
            E++R SQ+    T + FTF++V   +YL +T ++    +  E    R F R
Sbjct: 177 EEIMRHSQIGVTVTKEPFTFYMVAACIYLGLTVLAMTGMHFMEKRAARGFAR 228


Lambda     K      H
   0.327    0.141    0.403 

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: 116
Number of extensions: 2
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: 240
Length of database: 230
Length adjustment: 23
Effective length of query: 217
Effective length of database: 207
Effective search space:    44919
Effective search space used:    44919
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: 46 (22.3 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