GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Shewanella sp. ANA-3

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 7026373 Shewana3_3515 ABC transporter related (RefSeq)

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



>FitnessBrowser__ANA3:7026373
          Length = 349

 Score =  183 bits (465), Expect = 6e-51
 Identities = 114/307 (37%), Positives = 180/307 (58%), Gaps = 18/307 (5%)

Query: 2   ATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGA 61
           +TL L  V+  Y       LK ++L +  GE L L+GPSGCGK+TL+  +AGL+ IS G 
Sbjct: 3   STLNLHQVHSDYQG--QQVLKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGE 60

Query: 62  ILVDDADISG----MSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVA 117
           I ++   +SG    +  + R I M+FQ YAL+P ++V +NI FG  + K+  A+    + 
Sbjct: 61  IQINGKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFG--VAKLTPAQRKARLD 118

Query: 118 RVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTE 177
            +  L+++E L  R P +LSGGQQQRV++ RALA  P++ L DEP SN+DA++R  M  E
Sbjct: 119 DMLALVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAE 178

Query: 178 MKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIG 237
           ++ + ++   + V+VTH + EA    D +A+   G+I Q G  +++Y  P + +VA F+G
Sbjct: 179 IRSILKQRNVSAVFVTHSKDEAFVFADTLAIFNQGVIVQHGRAENLYAAPNSRYVADFLG 238

Query: 238 SPPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGE 297
           S   N++P  +   DG  + +   G+ R   PL    A   + +V L  RP+Q+ L+  +
Sbjct: 239 SG--NYLPAEV--IDGHSV-VTPIGELRSLTPLSQSHA--FNGQVFL--RPQQLALSADD 289

Query: 298 ANGLPTI 304
           A G+ TI
Sbjct: 290 A-GVGTI 295


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: 282
Number of extensions: 11
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: 386
Length of database: 349
Length adjustment: 30
Effective length of query: 356
Effective length of database: 319
Effective search space:   113564
Effective search space used:   113564
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: 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