GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtrB in Mesorhizobium ciceri WSM1271

Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate YP_004139565.1 Mesci_0342 TRAP dicarboxylate transporter subunit DctM

Query= TCDB::P74224
         (445 letters)



>NCBI__GCF_000185905.1:YP_004139565.1
          Length = 593

 Score =  335 bits (860), Expect = 2e-96
 Identities = 213/522 (40%), Positives = 295/522 (56%), Gaps = 104/522 (19%)

Query: 7   LGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFD--------PIFLSAMPQRI 58
           + P+MF   ++FL  GYPVAFSL    ++F  IG  L  +         P+ L A+P   
Sbjct: 8   MAPIMFASLIIFLLIGYPVAFSLAANGLMFFFIGVLLSPYSGGSINLAWPL-LHALPDNF 66

Query: 59  FG--IMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLA 116
           +G  +M+N TLLAIPFF F+G +LERSG+AE LL+T+G + G +RGGLA AVI VG +LA
Sbjct: 67  YGSRVMSNDTLLAIPFFTFMGIVLERSGMAEDLLDTIGQLFGPIRGGLAYAVIFVGALLA 126

Query: 117 ATTGVVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGV 176
           ATTGVVAA+V+AMGLISLPIMLRYGY + LASGVI ASGTL QIIPPS+VLIVLADQLG 
Sbjct: 127 ATTGVVAASVIAMGLISLPIMLRYGYDRRLASGVIAASGTLAQIIPPSLVLIVLADQLGR 186

Query: 177 SVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLP 236
           SVGD++ G+L+PGL++ G +  Y+LI++ ++P+  PALP E R +G   +          
Sbjct: 187 SVGDMYAGALIPGLVLTGLYMSYILIMSIIRPNSMPALPLEARTLGHGVM---------- 236

Query: 237 PLVLILLVLGSIFFG---IASPTEAGAVGSIGAIA-------LAHFNQRLNWKALWEVCD 286
            L++ LLV  ++ +      +P        +GA A       +A  ++RLN+  +  +  
Sbjct: 237 SLLVALLVTSAVSYAAYRYLAPAHGDNADILGATAGVLFIYIVAIADKRLNFNMMSRLAQ 296

Query: 287 ATL--RITSMVMLILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMI------ 338
             +   I  + ++ L+  T F  +    EG   M  + A       G L++ ++      
Sbjct: 297 QVIIVLIPPLALIFLVLGTIFLGIATPTEGGA-MGSVGALFMAAAKGRLSLDVVKQALAS 355

Query: 339 -------TIFIL-------------------------------GFFI------------- 347
                   +FIL                               GF I             
Sbjct: 356 TTRLSSFVLFILIGARVFSLTFYGVNGHIWVEHLLTSLPGGEVGFLIGVNMLVFFLAFFL 415

Query: 348 DFFEIAFIVLPLFKPVAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAP---- 403
           DFFE+AFI++PL  P A+ L +DLIW+GV++G N+QTSF+ PPFGFALFYLR VA     
Sbjct: 416 DFFELAFIIVPLLAPAADKLGIDLIWFGVLLGVNMQTSFMHPPFGFALFYLRSVAARVPY 475

Query: 404 ---------ASLTTGQIYRGAVPFIGLQVLVLLLIIIFPALI 436
                    A +TTGQIY GAVPF+ +QV+++ L I FP ++
Sbjct: 476 LDRLTGKQIAPVTTGQIYWGAVPFVCIQVIMIGLTIAFPQMV 517


Lambda     K      H
   0.331    0.148    0.443 

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: 861
Number of extensions: 53
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 445
Length of database: 593
Length adjustment: 35
Effective length of query: 410
Effective length of database: 558
Effective search space:   228780
Effective search space used:   228780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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