GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Marinobacter adhaerens HP15

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__Marino:GFF3011
          Length = 372

 Score =  197 bits (501), Expect = 4e-55
 Identities = 124/373 (33%), Positives = 202/373 (54%), Gaps = 28/373 (7%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M+ + + ++ K +  G  E + +  + I I SG    ++GPSG GK+T +  IAGLE  T
Sbjct: 1   MSQLELRSIRKTYP-GVAE-ETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETIT 58

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
            G I  D + +S+     M P+ R IAMVFQ++ALYP M+V +NIAF LK+  +PK +I+
Sbjct: 59  DGSIVLDGKDIST-----MEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEID 113

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            +V+ V++ L +S ++N+ P  LSGGQ QR A+ RAL + P++ L DEP SNLDA++R  
Sbjct: 114 QEVERVADLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVE 173

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            R  ++K+ +  K T + V+HD  +   +A++  V+ +G+  Q+GTP E+Y+ P    +A
Sbjct: 174 MRTEIKKLHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVA 233

Query: 241 RLTGEINL-------------IQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDL 287
              G   +             +QA++  N+     L VP    +  G+  +++G+RP+ +
Sbjct: 234 GFMGSPAMSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGK-KVILGIRPEHI 292

Query: 288 TLSDTLLDKYIDMGIVK----VKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIET 343
           T      D+  D  +V        V+   G   I +  + D N+   +D E P+  G   
Sbjct: 293 TQPQ---DQKNDQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETA 349

Query: 344 HLLAKPNKVKIFD 356
            L+    KV  FD
Sbjct: 350 ELMFDMKKVVFFD 362


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: 288
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: 372
Length adjustment: 30
Effective length of query: 341
Effective length of database: 342
Effective search space:   116622
Effective search space used:   116622
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