GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Desulfovibrio vulgaris Hildenborough

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>MicrobesOnline__882:208681
          Length = 349

 Score =  192 bits (489), Expect = 9e-54
 Identities = 123/358 (34%), Positives = 198/358 (55%), Gaps = 21/358 (5%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M+TI ++ +S+ +     +V+AVD+VS  ++ G    +LGPSG GK+T LRLIAGLE  T
Sbjct: 1   MSTIVLDKVSRHWG----DVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVT 56

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
           SG I      V++     + P +R +AMVFQ++AL+P++TV DNI F L + KVP  + +
Sbjct: 57  SGRILIGGRDVTN-----LPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQ 111

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            ++    E LGL  +L R P ELSGGQ QR A+ RALV +  V L+DEP SNLDA++R+ 
Sbjct: 112 KRLDRAVEILGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQE 171

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            R  +R +Q+   +T + V+HD  +  ++A++  ++  G+  Q  TPTE+Y  PAT    
Sbjct: 172 MRREIRALQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAG 231

Query: 241 RLTG--EINLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKYI 298
              G   +NL++ +  ++   +A  +     +     ++ ++G+RP+ + + D       
Sbjct: 232 SFIGTPPMNLVRLQGNDDGIRVAGSR--SGRVTCHAGADCMLGIRPEHIRIVD------- 282

Query: 299 DMGIVKVKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAKPNKVKIFD 356
           D     V+ V Y  G   ++   +  E + ++V        G E +L      V IFD
Sbjct: 283 DGWRAVVESVEY-LGSNSVLSCRVGSEELSVVVHGVTDTVVGAEIYLHCPEEHVHIFD 339


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: 216
Number of extensions: 4
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: 349
Length adjustment: 29
Effective length of query: 342
Effective length of database: 320
Effective search space:   109440
Effective search space used:   109440
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