GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Azospirillum brasilense Sp245

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate AZOBR_RS28110 AZOBR_RS28110 C4-dicarboxylate ABC transporter

Query= TCDB::Q848I3
         (444 letters)



>FitnessBrowser__azobra:AZOBR_RS28110
          Length = 457

 Score =  462 bits (1190), Expect = e-135
 Identities = 224/415 (53%), Positives = 305/415 (73%)

Query: 2   TTRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVS 61
           T  +  YK+LYFQV+V + +GIL GHF+P  G +LKPLGDGF+KL+KM+IAP++FCT+VS
Sbjct: 13  TKPKAFYKALYFQVVVGLTLGILAGHFWPDLGASLKPLGDGFVKLVKMMIAPVVFCTIVS 72

Query: 62  GIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAA 121
           GI  + + + +GKT   ++  F  ++  ALLIGL  V +++PG GMH+  ++LD +  A 
Sbjct: 73  GITSLNDTREIGKTLVKSMALFYALTVAALLIGLAAVMIIEPGVGMHVSAASLDPTVAAR 132

Query: 122 YVTAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFID 181
           Y           F+L++IP++  GAFA G++L VL+ SV+ GF L R+G  G+PV+  I+
Sbjct: 133 YAKQAAPVGFTDFVLHIIPHSFFGAFAEGEVLPVLLISVLVGFGLTRVGKAGEPVVQGIE 192

Query: 182 RFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLG 241
            F+HV+F     IMKLAPIGA GAMAFT+G YG+ S+  LG L++ FY+ C +F++VV+G
Sbjct: 193 SFSHVLFAAFGFIMKLAPIGAFGAMAFTVGKYGIDSIGSLGLLILTFYVACGVFLMVVIG 252

Query: 242 AICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYS 301
            + R HGFS+ K++RY REELLIVLGTSSSE  LPR+L K+E LG KK V GLV+P GYS
Sbjct: 253 TLARLHGFSLWKVLRYFREELLIVLGTSSSEPVLPRVLQKLEALGCKKGVSGLVLPMGYS 312

Query: 302 FNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLS 361
           FNLDGT+IYLT+A++FIAQA D H+       +L V+LL+SKGAAGVTGSGF+ L ATL+
Sbjct: 313 FNLDGTAIYLTLASLFIAQACDIHLSGGQIFAMLGVMLLTSKGAAGVTGSGFVALVATLT 372

Query: 362 AVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAEL 416
            +  LPVAG+AL++GIDRFMSEARALT+++ N VA++VV+ W    D + LQ EL
Sbjct: 373 VMPDLPVAGVALLVGIDRFMSEARALTSIISNCVASIVVSIWENACDREVLQREL 427


Lambda     K      H
   0.326    0.142    0.402 

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: 595
Number of extensions: 30
Number of successful extensions: 1
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: 444
Length of database: 457
Length adjustment: 33
Effective length of query: 411
Effective length of database: 424
Effective search space:   174264
Effective search space used:   174264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 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