GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtrB in Phaeobacter inhibens BS107

Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate GFF1982 PGA1_c20160 TRAP transporter, subunit DctM

Query= TCDB::P74224
         (445 letters)



>FitnessBrowser__Phaeo:GFF1982
          Length = 785

 Score =  154 bits (390), Expect = 7e-42
 Identities = 130/412 (31%), Positives = 192/412 (46%), Gaps = 94/412 (22%)

Query: 102 GGLALAVILVGTMLAAT--TGVVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQ 159
           GG+  A  L    L A     + AA  +  GL  L +++  G    +  GV  +S     
Sbjct: 394 GGVTQATKLTEEELEAAKIAKIDAAAPIGTGLTVLMVLM--GLVLAVGRGVSPSSDPKPL 451

Query: 160 IIPP-SVVLIVLADQLGVSVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPA-- 216
           I+    V+LI L D + ++       +  PG+         VL+IA       P L A  
Sbjct: 452 ILGAIGVLLIALVDVVAIAP------TTSPGIT--------VLLIA------LPTLLALY 491

Query: 217 EVRNIGGQELRRRIVQVMLPPLVLILLVLGSIFFGIASPTEA------GAV--------- 261
             R   G+  R  +++V+ PPL+LI+ VLGSI  GI +PT A      GA+         
Sbjct: 492 GCRIAAGRSARNDLIRVVFPPLILIVAVLGSILGGITNPTPAAALGAGGAIMLAAYRKLQ 551

Query: 262 --GSIGAIAL-------------AHFNQRLNWKA-------------------------- 280
             G  G I +              +F+ R+N ++                          
Sbjct: 552 DQGKSGKIIIWATFAVAICILVGVNFDLRINGRSGVSAETVIAFGVAYGAYLFALFGLLY 611

Query: 281 ----------LWEVCDATLRITSMVMLILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQI 330
                     L  V   T ++TSMV  IL+GS   +LV     G+ ++   L +      
Sbjct: 612 GCWVLFKGGVLTPVVRETAKVTSMVFTILIGSQLLNLVVISFGGEHYIQQFLKSFDSELK 671

Query: 331 GFLAISMITIFILGFFIDFFEIAFIVLPLFKPVAEALNLDLIWYGVIVGANLQTSFLTPP 390
            FL + M+ +FILGF +DF EI +IV+P+  PV    + D  W  ++V  NLQTSFLTPP
Sbjct: 672 VFLIV-MVVLFILGFVLDFLEIIYIVIPIVGPVIYGGSFDPKWVTIMVAVNLQTSFLTPP 730

Query: 391 FGFALFYLRGVAPASLTTGQIYRGAVPFIGLQVLVLLLIIIFPALINWLPSL 442
           FGFALFYLRGVAP  +TT  IYRG +PF+ +QV+ L ++ +FP+++  +P+L
Sbjct: 731 FGFALFYLRGVAPKEVTTAHIYRGVLPFVLIQVVGLGILWMFPSIVTIVPAL 782



 Score =  152 bits (385), Expect = 3e-41
 Identities = 89/195 (45%), Positives = 118/195 (60%), Gaps = 28/195 (14%)

Query: 51  LSAMPQRIFGIMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVIL 110
           ++ M +R+    +  TLLA+  F+ +G  LERS IA  LL TM  + G L GGLA+++++
Sbjct: 110 VNRMNERVLAGASIETLLAVLMFVLMGITLERSKIANDLLTTMARVFGPLPGGLAVSIVV 169

Query: 111 VGTMLAATTGVVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVL 170
           VG  LAA+TG+V ATVV MGL++LP MLR  YS ELA+GVI ASGTLGQIIPPS+V+++L
Sbjct: 170 VGAFLAASTGIVGATVVTMGLLALPTMLRNNYSPELATGVIAASGTLGQIIPPSIVIVLL 229

Query: 171 ADQLG----------------------------VSVGDLFIGSLLPGLMMAGSFALYVLI 202
               G                            VSVG LF  +LLPG+M+A  +ALY   
Sbjct: 230 GTLAGDLYSTAQEARAQEFGCSDALTYLGEPAVVSVGTLFQAALLPGIMLALLYALYAFG 289

Query: 203 IAWLKPDLAPALPAE 217
            A L P+ APA+  E
Sbjct: 290 YALLNPEKAPAVVLE 304


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: 911
Number of extensions: 42
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 4
Length of query: 445
Length of database: 785
Length adjustment: 37
Effective length of query: 408
Effective length of database: 748
Effective search space:   305184
Effective search space used:   305184
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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