GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Pseudomonas stutzeri RCH2

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__psRCH2:GFF857
          Length = 371

 Score =  330 bits (847), Expect = 3e-95
 Identities = 180/357 (50%), Positives = 231/357 (64%), Gaps = 28/357 (7%)

Query: 17  VGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76
           + S+ L+ I K++    + + IDLD++DGEFV+FVGPSGCGKSTLLR IAGLED TSG +
Sbjct: 1   MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60

Query: 77  QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136
            ID   V  + P  R + MVFQSYALYPH+TV +NM  GLK A V K EI+ +V   A +
Sbjct: 61  LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120

Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196
           L L+  L R+P +LSGGQRQRVAIGR +VREPK+FLFDEPLSNLDA LRV  R+EIARLH
Sbjct: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180

Query: 197 RSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMN 256
           + +++TMIYVTHDQVEAMTLADKIVVLNAG I QVG P+ LY+ P N FVAGF+GSPQMN
Sbjct: 181 QRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMN 240

Query: 257 FIE--------------------------AAKLGDGEAKTIGIRPEHIGLSRESG-DWKG 289
           F+E                           + +  G+  T+GIRPEH  +  E+   + G
Sbjct: 241 FVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDEADFTFHG 300

Query: 290 KVIHVEHLGADTIIYIESETV-GLLTVRLFGEHRYATDDIVHATPVIGSMHRFDADG 345
           ++   E LG   ++Y+  E +  ++T+ + G  R    +   A       H F  +G
Sbjct: 301 QITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFRENG 357


Lambda     K      H
   0.320    0.137    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: 351
Number of extensions: 16
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: 352
Length of database: 371
Length adjustment: 29
Effective length of query: 323
Effective length of database: 342
Effective search space:   110466
Effective search space used:   110466
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