GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Shewanella loihica PV-4

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__PV4:5208462
          Length = 378

 Score =  216 bits (550), Expect = 8e-61
 Identities = 122/323 (37%), Positives = 192/323 (59%), Gaps = 24/323 (7%)

Query: 2   VRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61
           V + ++ VSK+F    V A+D+V++NI  GE F +LG SG+GK+T +R++AG + P+ G 
Sbjct: 19  VLLKIERVSKLFDD--VRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGR 76

Query: 62  LYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRV 121
           +Y D + +       +PP +R I M+FQ++AL+P++T  +NIAF L   KM K EI +RV
Sbjct: 77  IYLDGQDITD-----MPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRV 131

Query: 122 EEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARA 181
           +E+ K++ +       P +LSGGQ+QRVALAR+L K P LLLLDEP   LD ++R   + 
Sbjct: 132 KEMLKLVHMEPYAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQL 191

Query: 182 LVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLI 241
            V ++   +GVT ++V+HD  +   +A+R+ ++  G + Q G P D+Y++P +  VA  I
Sbjct: 192 EVVDILEAVGVTCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPANRMVAEFI 251

Query: 242 GEINELEGKVTN---EGVVIGSLRFP----------VSVSSDRAIIGIRPEDVKLSKDVI 288
           G +N  EG +     + VVI     P           SV + +  + IRPE   +S++  
Sbjct: 252 GSVNLFEGDIVEDEVDHVVINVANIPQPFYVGYGVSTSVDTTQVWVAIRPEKTHISREQP 311

Query: 289 KD-DSWILVGKGKVKVIGYQGGL 310
           +D  +W     GKV+ I Y GG+
Sbjct: 312 EDARNWC---AGKVEDIAYLGGI 331


Lambda     K      H
   0.319    0.139    0.390 

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: 316
Number of extensions: 14
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: 353
Length of database: 378
Length adjustment: 30
Effective length of query: 323
Effective length of database: 348
Effective search space:   112404
Effective search space used:   112404
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