GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Snodgrassella alvi wkB2

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_025329853.1 SALWKB2_RS01070 sulfate ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_000600005.1:WP_025329853.1
          Length = 360

 Score =  183 bits (464), Expect = 7e-51
 Identities = 107/317 (33%), Positives = 186/317 (58%), Gaps = 16/317 (5%)

Query: 3   TIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSG 62
           +IR++ L+K +     + +A+ N+++ + +G    +LGPSG GKTT LR+IAGLE   SG
Sbjct: 2   SIRIKQLNKYYG----DYQALQNINLQVPTGSLTALLGPSGCGKTTLLRIIAGLERADSG 57

Query: 63  YIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPL----KLAKVPKDK 118
            ++F ++ VS+     +   +R +  +FQ++AL+ +MTVFDN+AF L    K  +  K +
Sbjct: 58  ELFFADDEVSN-----LHVRERRVGFMFQHYALFRHMTVFDNVAFGLQVLPKRIRPNKAE 112

Query: 119 IENKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIR 178
           I ++V E+ + + L  +   YP++LSGGQ QR A+ARAL   PK+LLLDEPF  LDA++R
Sbjct: 113 IADRVHELLQLVQLDWLAKVYPQQLSGGQRQRIALARALATRPKLLLLDEPFGALDAKVR 172

Query: 179 ESARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDL 238
           +  R  + +I  +  +T+++V+HD  +   +A +  V+  GK  Q G  + +Y+ P    
Sbjct: 173 KELRQWLLEIHHQLGITSVLVTHDQEEALEMAEQIVVMNQGKVEQSGAASSLYDNPENVF 232

Query: 239 IARLTGEINLIQAKIIENNAI-IANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKY 297
           +    GE+N+ +   IE+  + + +   P+   E K + N+ + +RP ++ +   + D  
Sbjct: 233 VTEFLGEVNVFEDACIEHGQLCLGHYHEPITTGE-KARQNVAVYIRPQEVQVLTHIQDNI 291

Query: 298 IDMGIVKVKLVSYGAGI 314
           I    V+ K+ + GA I
Sbjct: 292 IASACVE-KIHAIGAQI 307


Lambda     K      H
   0.317    0.136    0.374 

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: 270
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: 371
Length of database: 360
Length adjustment: 30
Effective length of query: 341
Effective length of database: 330
Effective search space:   112530
Effective search space used:   112530
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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