GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Pseudomonas baetica a390

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate WP_095190355.1 C0J26_RS26645 C4-dicarboxylate transporter DctA

Query= CharProtDB::CH_014038
         (428 letters)



>NCBI__GCF_003031005.1:WP_095190355.1
          Length = 437

 Score =  408 bits (1049), Expect = e-118
 Identities = 205/412 (49%), Positives = 294/412 (71%), Gaps = 1/412 (0%)

Query: 7   KSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMES 66
           +S++ QV+  + +GI+ G   PE   Q+KPLGDGF+KLIKM+I  ++FC VV+GI+G   
Sbjct: 7   RSIFLQVVLGLVLGIVCGLTLPEYSAQLKPLGDGFIKLIKMLIGLIVFCVVVSGISGAGD 66

Query: 67  MKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKD 126
           +K VGR G  +++YFE+++TIAL+IGL+       G+G N+    L A  +   A++++ 
Sbjct: 67  LKKVGRIGLKSVIYFEVLTTIALVIGLVFAFSTGIGSGANIHLEQLSAADMGDLAERSQH 126

Query: 127 QGIVA-FIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVI 185
                 F+MD+IP SVIGAFA  NILQVLLF+VLFG AL+ +G     I  +I   S VI
Sbjct: 127 MHTTTQFLMDLIPTSVIGAFADNNILQVLLFSVLFGSALNLVGEAASGISRLINELSHVI 186

Query: 186 FGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKAT 245
           F I+ MI+RLAPIG FGA+AFT  KYG+ +L  LG L+  FY+TCI FV ++LG + +A+
Sbjct: 187 FRIMGMIVRLAPIGVFGAIAFTTSKYGLDSLQHLGSLVGLFYLTCIAFVSVILGVVMRAS 246

Query: 246 GFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGT 305
           G  ++  ++Y+REELLIV+GT+SS++ LP+++ K+E LG   S VGLVIPTGYSFNLDG 
Sbjct: 247 GLRMWPLLKYLREELLIVMGTASSDAVLPQIMRKLEHLGIGSSTVGLVIPTGYSFNLDGF 306

Query: 306 SIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLP 365
           SIYLT+A VFIA AT + + +   +T+L+V L++SKGA G+ GS  ++LAATL+A+  +P
Sbjct: 307 SIYLTLAIVFIANATGTPLAMTDLLTILLVSLITSKGAHGIPGSALVILAATLTAIPAIP 366

Query: 366 VAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNR 417
           V GL L+L +D FM   RALTNL+GN VAT+ +A+W K++D ++ + VL+ +
Sbjct: 367 VVGLVLVLAVDWFMGIGRALTNLIGNCVATVAIARWEKDIDVQRANKVLSGQ 418


Lambda     K      H
   0.327    0.142    0.401 

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: 568
Number of extensions: 37
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: 428
Length of database: 437
Length adjustment: 32
Effective length of query: 396
Effective length of database: 405
Effective search space:   160380
Effective search space used:   160380
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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