GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Pseudomonas stutzeri RCH2

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components

Query= reanno::Smeli:SMc04256
         (361 letters)



>FitnessBrowser__psRCH2:GFF857
          Length = 371

 Score =  310 bits (795), Expect = 3e-89
 Identities = 166/361 (45%), Positives = 231/361 (63%), Gaps = 6/361 (1%)

Query: 1   MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60
           M SV++RD+  ++    +   ++LDI+ GEF+V +G SGCGKSTLL  IAGL D++ G +
Sbjct: 1   MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60

Query: 61  FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120
            I ++ V    PKDR +GMVFQSYALYP MTV +N++FGLK+A +   EI++RV+  +EI
Sbjct: 61  LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120

Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180
           LQ+  LL+RKP +LSGGQRQRVAIGR +VR+  VFLFDEPLSNLDA LR ++R+EI RLH
Sbjct: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180

Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240
           Q +++TMIYVTHDQ+EA+TLAD+I V+ +G I Q+  P+ +Y+ P+N FVAGF+GSP MN
Sbjct: 181 QRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMN 240

Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEH-VKVDEARDGEPT 299
           F           +        + +T     + + PG  + LG+RPEH V  DEA   + T
Sbjct: 241 FVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDEA---DFT 297

Query: 300 HQAVVDIEEPMGADNLLWLTF--AGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAES 357
               + + E +G  NLL+LT       +++ + G  R   G T           +F    
Sbjct: 298 FHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFRENG 357

Query: 358 E 358
           E
Sbjct: 358 E 358


Lambda     K      H
   0.320    0.137    0.392 

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: 419
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: 361
Length of database: 371
Length adjustment: 30
Effective length of query: 331
Effective length of database: 341
Effective search space:   112871
Effective search space used:   112871
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