GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Pseudomonas stutzeri RCH2

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__psRCH2:GFF3591
          Length = 369

 Score =  228 bits (582), Expect = 2e-64
 Identities = 130/297 (43%), Positives = 181/297 (60%), Gaps = 7/297 (2%)

Query: 4   LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63
           +  R + K+Y  G    ++++ L I  GEFL L+GPSG GK+T +  +AG ET + G IL
Sbjct: 11  VSFRGIQKSYD-GESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIL 69

Query: 64  VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123
           +D   I+ + P  RD+ MVFQ+YAL+P M+V +N+AF L +R M   +I E V R   ++
Sbjct: 70  LDGRAINNVPPHKRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMV 129

Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
           Q+E   +R P QLSGGQQQRVA+ RAL   P++ L DEPL  LD +LR +M+ E+K +H+
Sbjct: 130 QLEGFRNRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHE 189

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243
           RL  T VYVTHDQ EA+T+ D+VAV   G IQQ   P+ +Y  P N FVA+F+G    N 
Sbjct: 190 RLGVTVVYVTHDQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLGE--NNR 247

Query: 244 IPLR-LQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEAN 299
           +P   L R+       L  G+    L + +  AG     V L IRPE+++L    AN
Sbjct: 248 LPAHLLDRRGDSCTVKLGRGETVEALAVNVGAAG---TPVSLSIRPERVLLNGASAN 301


Lambda     K      H
   0.319    0.138    0.393 

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: 350
Number of extensions: 12
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: 386
Length of database: 369
Length adjustment: 30
Effective length of query: 356
Effective length of database: 339
Effective search space:   120684
Effective search space used:   120684
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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