GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PV4:5209833
          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:

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