GapMind for catabolism of small carbon sources

 

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

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__ANA3:7026050
          Length = 376

 Score =  215 bits (548), Expect = 1e-60
 Identities = 112/239 (46%), Positives = 159/239 (66%), Gaps = 6/239 (2%)

Query: 4   VLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLY 63
           + L +I K + GQ +  +   NLDIQ+ E    +GPSG GKTT LR+IAGLE    G ++
Sbjct: 3   IRLTNISKKF-GQFQ-ALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIH 60

Query: 64  IGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGL----KLRKVPKAEIDRRVQEA 119
            G+R V  V  +DR +  VFQNYAL+ HMTV  N+AFGL    K ++  KAEI +RV   
Sbjct: 61  FGNRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHL 120

Query: 120 AKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIR 179
            +++ + HL  R P+ LSGGQ+QR+AL RA+  +P+V L+DEP   LDAK+R ++R  +R
Sbjct: 121 LEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLR 180

Query: 180 KLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGS 238
            LH  L+ T ++VTHDQ EA+ + DR+VVM +G I+Q +TP  +Y+QP + FV  F+G+
Sbjct: 181 SLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGN 239


Lambda     K      H
   0.321    0.138    0.395 

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: 358
Number of extensions: 6
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: 384
Length of database: 376
Length adjustment: 30
Effective length of query: 354
Effective length of database: 346
Effective search space:   122484
Effective search space used:   122484
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: 50 (23.9 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