GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Pseudomonas simiae WCS417

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate GFF2490 PS417_12700 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF2754
         (331 letters)



>FitnessBrowser__WCS417:GFF2490
          Length = 367

 Score =  330 bits (847), Expect = 3e-95
 Identities = 182/358 (50%), Positives = 235/358 (65%), Gaps = 32/358 (8%)

Query: 1   MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60
           M  L++ N+ K F    ++K I+L V D EFVVFVGPSGCGKSTLLR+I+GLE+ + G I
Sbjct: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60

Query: 61  SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120
            + G+ +T   PAKR +AMVFQ+YALYPH+SVR+NM+ AL      K+ + ++V+EA+R+
Sbjct: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARI 120

Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180
           L L   L+R+P +LSGGQRQRVAIGRA+VR PK+FLFDEPLSNLDAALR+  RLE+ARLH
Sbjct: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180

Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240
           ++L A+MIYVTHDQ+EAMTLADK+VVL  GRIEQVG+P+ELY+ PAN FVA F+G P M 
Sbjct: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240

Query: 241 FVPAQ--------------------------RLGGNPGQFIGIRPEYARISPVGPLAGEV 274
           F+  +                           L       +GIRPE+  I+  G     V
Sbjct: 241 FLKGKVTRVESQSCEVQLDAGTLINLPLSGATLSVGSAVTLGIRPEHLEIASPGQTTLTV 300

Query: 275 IH--VEKLGGDT--NILVDMGEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDEAG 328
                E+LG DT  +++   GE LT   R+ G   +  GETL    DPA+C  FD  G
Sbjct: 301 TADVGERLGSDTFCHVITANGEPLTM--RIRGDMASQYGETLHLHLDPAHCHLFDTDG 356


Lambda     K      H
   0.320    0.137    0.391 

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: 366
Number of extensions: 13
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: 331
Length of database: 367
Length adjustment: 29
Effective length of query: 302
Effective length of database: 338
Effective search space:   102076
Effective search space used:   102076
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: 49 (23.5 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