GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Dyella japonica UNC79MFTsu3.2

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1562
          Length = 384

 Score =  177 bits (448), Expect = 6e-49
 Identities = 109/308 (35%), Positives = 175/308 (56%), Gaps = 23/308 (7%)

Query: 22  AVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEAVSSPRRVMMSP 81
           A+D+ S+ I  G    +LGPSG GK++ LR++AGL++P  G +  D   +     + +  
Sbjct: 17  ALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRDGTDL-----LALPA 71

Query: 82  EKRGIAMVFQNWALYPNMTVFDNIAFPLKL---AKVPKDK-IENKVKEVSEELGLSGVLN 137
           ++R I +VFQ++AL+P+MTV DNIAF L++   A+ P  + I  +V+++   + L  +  
Sbjct: 72  QRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLLRRVQLEELGR 131

Query: 138 RYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQRERKLTTL 197
           RYP +LSGGQ QR A+ARAL  +P +LLLDEPF  LDAQ+R + R  +R +QR   LTT+
Sbjct: 132 RYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRDLQRSLGLTTV 191

Query: 198 IVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLTGEINLIQAKIIENN 257
           +V+HD  +   +A++  V+  G+  Q+G P+EIY  PAT  +    G  N I+  +  + 
Sbjct: 192 LVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVGRANRIRGHVERDR 251

Query: 258 AIIANLKVPLNNMELKGQ---SNIVIGLRPDDLTLSDTLLD------KYIDMG--IVKVK 306
             +          EL G      I   LRP+ L L+   L       +++D+   + + +
Sbjct: 252 LHLGGHSF---QGELPGDLAGREIEAWLRPEHLALASRGLGGWTGRLQHLDLAGPVARAR 308

Query: 307 LVSYGAGI 314
           L  +G G+
Sbjct: 309 LAMHGDGL 316


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: 269
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: 384
Length adjustment: 30
Effective length of query: 341
Effective length of database: 354
Effective search space:   120714
Effective search space used:   120714
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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