GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Dechlorosoma suillum PS

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  180 bits (457), Expect = 5e-50
 Identities = 108/365 (29%), Positives = 198/365 (54%), Gaps = 23/365 (6%)

Query: 3   TIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSG 62
           +I + N++K F        A+D+VS++I +G    +LGPSG GKTT LR+IAG+E    G
Sbjct: 2   SIEIRNIAKRFGN----FVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEG 57

Query: 63  YIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLA----KVPKDK 118
            + F+    +      +   +R +  VFQ++AL+ +M VF+N+AF L++     +  + +
Sbjct: 58  QVMFEGSEATH-----LHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESE 112

Query: 119 IENKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIR 178
           I  +V ++   + L  + +RYP +LSGGQ QR A+ARAL  +PKVLLLDEPF  LD ++R
Sbjct: 113 IRKRVMDLLSLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVR 172

Query: 179 ESARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDL 238
           +  R  +R++  E  ++++ V+HD  +   +A++  V+  G+  Q+G+P E+Y  PA+  
Sbjct: 173 KELRRWLRRLHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPF 232

Query: 239 IARLTGEINLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKYI 298
           + +  G +N+  +++    A +A   VP       GQ  +   +RP D+ +      + +
Sbjct: 233 VYQFLGNVNVFHSRVHGAWAEVARDDVP------AGQEAVAF-IRPHDIDIDTVATPESL 285

Query: 299 DMGIVKVKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAKPNKVKIFDLN 358
           +  +  V+ +     +  I    + +  +++  + ++ L       +  KP +VK+F  N
Sbjct: 286 EAKVSYVQTIGPLVRVEVIHQGELVE--VELTRERQQVLGLTAGQQVWLKPRQVKVF-AN 342

Query: 359 GSNLI 363
           G   +
Sbjct: 343 GEGAV 347


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: 286
Number of extensions: 9
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 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