GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtrB in Arenimonas metalli CF5-1

Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate WP_034212615.1 N787_RS08375 TRAP transporter large permease subunit

Query= TCDB::P74224
         (445 letters)



>NCBI__GCF_000747155.1:WP_034212615.1
          Length = 460

 Score =  456 bits (1174), Expect = e-133
 Identities = 244/448 (54%), Positives = 307/448 (68%), Gaps = 22/448 (4%)

Query: 10  MMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMANGTLLA 69
           ++ +G    L  G+PVAF LGGVA+L A  G   GSFDP FL A P R+FG+M N TL+A
Sbjct: 13  LLLLGLFAGLASGFPVAFVLGGVALLAAGAGMLTGSFDPSFLEAFPNRVFGVMTNETLVA 72

Query: 70  IPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATVVAM 129
           +P F+F+G MLE+S IAE LLE +  + G +RGGL +AV+LVG +LAA+TG+V ATVVAM
Sbjct: 73  VPLFVFMGVMLEKSRIAESLLEAVASLFGQVRGGLVVAVLLVGALLAASTGIVGATVVAM 132

Query: 130 GLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLG-------------- 175
           GLISLP MLR GY   LASG I ASGTLGQIIPPS+VL++L DQLG              
Sbjct: 133 GLISLPTMLRNGYCPRLASGAICASGTLGQIIPPSIVLVLLGDQLGNAYQQAQLKQGIFA 192

Query: 176 ---VSVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQ 232
              +SVGDLF G+L+PGL + G +  Y L +AW +P  APA+ A +   G   L + IV 
Sbjct: 193 PETISVGDLFAGALVPGLGLVGLYLAYALWVAWRQPVRAPAV-ASLAPRGKLALAKAIV- 250

Query: 233 VMLPPLVLILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRIT 292
              P L LILLVLGSI  G A+ TEA AVG++GA   A  + +L W  L EV + T+R+T
Sbjct: 251 ---PALSLILLVLGSILGGFATATEAAAVGAVGATVFAAMHGQLGWARLREVSEQTVRVT 307

Query: 293 SMVMLILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEI 352
           +MV  ILLG+  FSLVFRG  GD  + + L  LPGG+ G +   M+ +F+LGF +DF EI
Sbjct: 308 AMVFAILLGAALFSLVFRGYGGDELVHEALTALPGGKWGAVVAVMLLMFLLGFVLDFIEI 367

Query: 353 AFIVLPLFKPVAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIY 412
            F+V+P+  PV  AL +D +W GV++  NLQTSFLTPPFGFALFYLRGVAP  L TG IY
Sbjct: 368 VFVVVPIVGPVLLALGVDPVWLGVMMAINLQTSFLTPPFGFALFYLRGVAPPELATGDIY 427

Query: 413 RGAVPFIGLQVLVLLLIIIFPALINWLP 440
           RG VPFIGLQ+L+L L+ +FP+L   LP
Sbjct: 428 RGVVPFIGLQLLMLALVALFPSLATALP 455


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: 674
Number of extensions: 40
Number of successful extensions: 4
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: 445
Length of database: 460
Length adjustment: 33
Effective length of query: 412
Effective length of database: 427
Effective search space:   175924
Effective search space used:   175924
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: 51 (24.3 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