GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Pseudomonas fluorescens GW456-L13

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate PfGW456L13_386 Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_386
          Length = 254

 Score =  245 bits (625), Expect = 8e-70
 Identities = 129/247 (52%), Positives = 177/247 (71%), Gaps = 3/247 (1%)

Query: 16  LEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLD 75
           L + +LHK YG  EVLKGV L  + G+V++LIG+SGSGK+T LRC+N LE    G + LD
Sbjct: 4   LTVENLHKSYGNHEVLKGVSLNARTGDVISLIGASGSGKSTFLRCINFLETPNDGAMSLD 63

Query: 76  GESIGY-HEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHK 134
            + I   H+ +G RV  + + + + R    M FQ FNL+ H+T L N+T+   +V  + K
Sbjct: 64  SQPIKMVHDHHGMRVADANE-LQRIRTRLAMVFQHFNLWSHMTVLDNITMAPRRVLGVSK 122

Query: 135 DEAVVLAEKWLERVGLLER-RDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDP 193
            +A   A ++L++VGL  R  D YP  LSGGQQQRVAIARA++M P +MLFDE TSALDP
Sbjct: 123 KDAEDRARRYLDKVGLPARVADQYPAFLSGGQQQRVAIARALSMEPEIMLFDEPTSALDP 182

Query: 194 ELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQS 253
           ELVGEVL VI+GLAE+G TM++VTHEM FA +VS++++F++QGR+EEQG P+++   P+S
Sbjct: 183 ELVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSNQVLFLHQGRVEEQGAPEDVLGNPKS 242

Query: 254 PRLAEFL 260
            RL +FL
Sbjct: 243 ERLKQFL 249


Lambda     K      H
   0.319    0.135    0.379 

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: 186
Number of extensions: 9
Number of successful extensions: 3
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: 265
Length of database: 254
Length adjustment: 24
Effective length of query: 241
Effective length of database: 230
Effective search space:    55430
Effective search space used:    55430
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 (21.8 bits)
S2: 47 (22.7 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