GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsA in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate H281DRAFT_01454 H281DRAFT_01454 carbohydrate ABC transporter substrate-binding protein, CUT1 family

Query= reanno::WCS417:GFF4324
         (428 letters)



>FitnessBrowser__Burk376:H281DRAFT_01454
          Length = 412

 Score =  244 bits (622), Expect = 5e-69
 Identities = 156/423 (36%), Positives = 215/423 (50%), Gaps = 21/423 (4%)

Query: 7   LAVAISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWKDGAVAG 66
           L   ++  ++  + A+A   K  V  +HWWTSGGE AA+        K G  W D AVAG
Sbjct: 8   LRAMVAALAMHGVLAYAEPLKANV--IHWWTSGGESAAIRQFADAYNKAGGQWIDNAVAG 65

Query: 67  GGGATAMTVLKSRAVAGNPPGVAQIK-GPDIQEWASTGLLDTDVLKDVAKEEKWDSLLDK 125
              A +  +  +R V G+PP  AQ        +    GLL+   + DVA +E W  +  +
Sbjct: 66  ADQARSTAI--NRIVGGDPPTAAQFNTSKQFHDLIDQGLLNN--VDDVAAKENWSGVFPQ 121

Query: 126 KVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAGFI 185
            + D++K +G Y A PV+IH   W + +   F+KAGIT  P +  EF A   KL+AAG I
Sbjct: 122 SILDSIKVKGHYYAAPVDIHMPAWFFYSKPAFQKAGITAEPQSYDEFIADLGKLRAAGVI 181

Query: 186 PLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKVATYMD 245
           PLA GGQPWQ+   F+AV+  V G D Y K   D D  A+      K L   K++  ++D
Sbjct: 182 PLAFGGQPWQEKITFDAVLADVGGPDLYLKVYRDHDANAVKSDAFKKVLIAFKRLHDFVD 241

Query: 246 VDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKAFTYNI 305
               G++WN     VI+GKAG+QIMGDWAK E++AAK+ AGK++ C  FPG      Y +
Sbjct: 242 AGSPGRNWNDATALVISGKAGVQIMGDWAKGEFSAAKQSAGKEFGC--FPGFGPHSPYLV 299

Query: 306 --DSLAVFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGFDSC 363
             D     K  +  T   Q  +A V+     Q  FS  KGSIP+R D    +D+   D C
Sbjct: 300 AGDVFVFPKSDNASTVKAQNLLATVMTSPPAQVAFSAKKGSIPIRPD----VDAGSLDIC 355

Query: 364 AQTAAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADTAKKLGAA 423
           A+      + D       P M  +  T    QGA  DVVTN+ N  ++   D  K    A
Sbjct: 356 AKEGIA-IMKDKSRQLPNPEMLLSPDT----QGALIDVVTNFWNKNQS-VDDAQKAFAGA 409

Query: 424 IKS 426
           +KS
Sbjct: 410 LKS 412


Lambda     K      H
   0.314    0.131    0.388 

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: 492
Number of extensions: 23
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: 428
Length of database: 412
Length adjustment: 32
Effective length of query: 396
Effective length of database: 380
Effective search space:   150480
Effective search space used:   150480
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: 42 (22.0 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