GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araV in Pseudomonas fluorescens FW300-N1B4

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate Pf1N1B4_3974 ABC transporter, ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3974 ABC transporter,
           ATP-binding protein
          Length = 341

 Score =  209 bits (531), Expect = 1e-58
 Identities = 118/310 (38%), Positives = 188/310 (60%), Gaps = 26/310 (8%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M  +++ENL K +     E+ AV   +++++ G    +LGPSG GKTT L++IAG  E +
Sbjct: 1   MAFVQLENLGKRYG----EIDAVVATNLSVEKGEFVSLLGPSGCGKTTTLQMIAGFVEVS 56

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
           SG I  D   ++  +     P  RG+ +VFQ++AL+P+MTV DN+AF L++ KVP D+++
Sbjct: 57  SGRIVLDGRDITHAK-----PASRGLGVVFQSYALFPHMTVRDNVAFGLRMRKVPNDELQ 111

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            +V  V + + L+    RYP+ELSGGQ QR A+ARALV +P VLLLDEP SNLDA +RE 
Sbjct: 112 QRVDRVLKLVRLNQHAERYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREE 171

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            +  +R+IQRE  +TTL+V+HD ++  +I+++  V+  G+  QI  P  +YE+P T+ I+
Sbjct: 172 MQFEIRRIQREVGITTLMVTHDQSEALSISDRVVVMQAGRITQIDAPYTLYEHPRTEFIS 231

Query: 241 RLTGEINLIQAKIIENNAI-IANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKYID 299
              G+ NL+  +      + + N          +    + + LRP+ + L D      + 
Sbjct: 232 GFVGKANLLPGERDSAGVVQVCN----------RDNGELTLSLRPEKIDLRD------VG 275

Query: 300 MGIVKVKLVS 309
           +G ++ K+VS
Sbjct: 276 LGRLQGKIVS 285


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: 282
Number of extensions: 7
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: 371
Length of database: 341
Length adjustment: 29
Effective length of query: 342
Effective length of database: 312
Effective search space:   106704
Effective search space used:   106704
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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