GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Halomonas xinjiangensis TRM 0175

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  198 bits (504), Expect = 2e-55
 Identities = 124/361 (34%), Positives = 194/361 (53%), Gaps = 24/361 (6%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M +I++  L K +      V+AV  + + I  G    ++GPSG GK+T LR++AGLE  T
Sbjct: 1   MASIQLTGLKKTYAGN---VEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETIT 57

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
            G +  D+  V+      + P +R IAMVFQN+ALYP+MTVF N+A+ LK   V +++IE
Sbjct: 58  DGTLKIDDRVVND-----LEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIE 112

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            +V + +  L +   L R P++LSGGQ QR A+ RALV++P   L DEP SNLDA++R  
Sbjct: 113 RRVHDAAAMLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQ 172

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            R  ++++QR  K T+L V+HD  +   + ++  V+  G   Q+GTP E+YE PA+  +A
Sbjct: 173 MRVEIKQLQRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVA 232

Query: 241 RLTGE--INLIQAKIIEN---NAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLD 295
              G   +N++    +     N ++ +L    +          VIG+RPDDL +     D
Sbjct: 233 TFIGSPAMNMLPVAYLRERGANGLLDHLAADTD----------VIGIRPDDLRIEAPDED 282

Query: 296 KYIDMGIVKVKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAKPNKVKIF 355
             +  G V++   + GA     V    +D+   I   A  P+  G        P+ +  F
Sbjct: 283 HLVVTGTVEL-FEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMRFHVLPSALHPF 341

Query: 356 D 356
           +
Sbjct: 342 N 342


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: 278
Number of extensions: 10
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: 354
Length adjustment: 29
Effective length of query: 342
Effective length of database: 325
Effective search space:   111150
Effective search space used:   111150
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.

Links

Downloads

Related tools

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