GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Echvi_1871 in Shewanella loihica PV-4

Align SSS sodium solute transporter (characterized, see rationale)
to candidate 5209833 Shew_2286 SSS family solute/sodium (Na+) symporter (RefSeq)

Query= uniprot:L0FZF3
         (547 letters)



>lcl|FitnessBrowser__PV4:5209833 Shew_2286 SSS family solute/sodium
           (Na+) symporter (RefSeq)
          Length = 519

 Score =  535 bits (1377), Expect = e-156
 Identities = 275/545 (50%), Positives = 377/545 (69%), Gaps = 31/545 (5%)

Query: 5   TLDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAEQ 64
           TLD+ + + Y L ++ + + +SR+ K H +D+KDYFLA KALPWWA+GASLIASNISAEQ
Sbjct: 4   TLDIGILLVYALGLLGLALWISRQDKRHERDTKDYFLAGKALPWWAIGASLIASNISAEQ 63

Query: 65  FIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVRTV 124
            IGMSGSG+A+GLAI++YEWMAA TL++V  + LPI++K  IYTMPQ+L +R+D RV+T 
Sbjct: 64  IIGMSGSGYAIGLAIASYEWMAAITLILVGKYMLPIFIKNEIYTMPQYLEQRFDKRVKTT 123

Query: 125 MAIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAVAWTD 184
           +A+FWL +Y+ VNLT+VL+LG L++ET+ G+   YG++ LALF++ YS+YGGLKAVA+TD
Sbjct: 124 LALFWLSVYILVNLTAVLWLGGLAIETVAGIDWLYGMVFLALFSLAYSLYGGLKAVAYTD 183

Query: 185 VVQVVFLVAGGLATTYLALSLVGDGD-VWEGIGILRKAAPSHFSMIIEKGEMMIPDGSGG 243
           ++QVV L+ GGL  +YLAL  V DG  V  G   L  A P HF MI+ +           
Sbjct: 184 IIQVVLLIFGGLLLSYLALDRVADGQGVLAGFDRLSSALPEHFEMILSQ----------- 232

Query: 244 SRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLKLLMP 303
           S   Y+ LPG+SVL+GG+WI+N++YWG NQYI QRALAAKS+ EAQ G+ FA +LKLLMP
Sbjct: 233 SNPHYMSLPGISVLVGGLWIMNISYWGFNQYIIQRALAAKSVAEAQKGIAFAAYLKLLMP 292

Query: 304 LIVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLLHLLPPGLKGLAFAALT 363
           LIVV+PGIAA ++                  GL   D+AYP+++ L+P G+KGL FAAL 
Sbjct: 293 LIVVLPGIAAVLL----------------YPGLESPDQAYPSMMALMPAGVKGLVFAALV 336

Query: 364 AAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIVA-PQLR 422
           AAIVSSLASM NS STIFT+DIY        SEG  V +GR++++++ +IA ++A P L 
Sbjct: 337 AAIVSSLASMTNSISTIFTMDIY-AMLRPAKSEGHYVLVGRLSSLISLLIALVMAQPLLG 395

Query: 423 QLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFKVITPNLP 482
           + +QAFQYIQE+TG  +PG+  IF+ G FW++ TS  AL AA+ +   S   +   P LP
Sbjct: 396 EFEQAFQYIQEFTGVFTPGIVVIFLTGMFWRRATSQGALAAALGSAIFSFGLRFYWPELP 455

Query: 483 FIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAIEVDAELFSTSTKFKVGAVLICGILVAL 542
           F+DR+G+VFL+   L + +SL  G+  +   ++ +    F T   F V A+ +  IL  L
Sbjct: 456 FMDRIGLVFLLCLALSVLVSLM-GRSLEEGASVALGGVSFKTGRAFNVSALGVVVILNFL 514

Query: 543 YSVFW 547
           Y  +W
Sbjct: 515 YVTWW 519


Lambda     K      H
   0.326    0.140    0.414 

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: 866
Number of extensions: 42
Number of successful extensions: 8
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: 547
Length of database: 519
Length adjustment: 35
Effective length of query: 512
Effective length of database: 484
Effective search space:   247808
Effective search space used:   247808
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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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