Alignments for a candidate for betS in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for betS in Marinobacter adhaerens HP15

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate GFF2851 HP15_2795 transporter, BCCT family protein

Query= SwissProt::G3XCN6
         (706 letters)



>FitnessBrowser__Marino:GFF2851
          Length = 531

 Score =  425 bits (1092), Expect = e-123
 Identities = 222/495 (44%), Positives = 311/495 (62%), Gaps = 10/495 (2%)

Query: 51  FKVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSML 110
           F ++  VF  +  +I  FV   +I P  A+ +    +   ++ F W +LLS  +F+   L
Sbjct: 25  FDIHNIVFPLTAILIVAFVVGTLIFPAGAKELLDSAKNGAIAVFDWGFLLSANLFVVFCL 84

Query: 111 FLAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFA----SPPE 166
            L F   G++++G  D++PEF  LSW AMLFAAGMG GLM+++V EP+ ++     +P  
Sbjct: 85  ALIFMPVGKIRIGGLDAKPEFSLLSWFAMLFAAGMGTGLMFWSVAEPVAYYTDWYGTPLG 144

Query: 167 AEPLTIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGI 226
            EP T    R AM  T +HWG+H WAIY++VGLSL++F +   LPLT+RS  +P+L + +
Sbjct: 145 VEPNTAEGARLAMGATMYHWGLHPWAIYAIVGLSLSFFAFNKGLPLTIRSAFFPILGDKV 204

Query: 227 HGPIGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIAT 286
            G  G+V+D  ++  T+FGLATSLGFG  Q  SG++YL  I   + +Q+ ++  VTA+AT
Sbjct: 205 WGWPGNVIDTVSVLATIFGLATSLGFGAQQAASGISYLFDIEGGLNIQVGVIAGVTAVAT 264

Query: 287 ISVVTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNI 346
           +SV+ G+  GVRILS  N+ +A LL+LFV+  GPT  + +        Y  ++   +   
Sbjct: 265 LSVIRGIHGGVRILSNANMIMAGLLLLFVIFAGPTLAVFQWLWDTSVSYASNMFSLSNPF 324

Query: 347 YAYEPRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMT 406
              E   W   WT+FYWAWWISWSPFVGMFIAR+S GRTVREFVTAVL +P + T  WM+
Sbjct: 325 GREEDTTWFHGWTVFYWAWWISWSPFVGMFIARVSHGRTVREFVTAVLIIPTIITLFWMS 384

Query: 407 VFGNTAI-YVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSS 465
            FG  A+  V   I  G L  +   ++S+A+FQ  E +    +TS + + LV  FFVTSS
Sbjct: 385 AFGGGALNQVQNEI--GVLGSEGLTEVSLAMFQMLENISLSGITSFIGITLVLTFFVTSS 442

Query: 466 DSGSLVIDTIASGGETATPALQRIFWCSLSGIVAAVLLSTGG---LTALQSATISTALPF 522
           DSGSLVID+I SGG+T  P  QRIFW    G +A VLL  GG   L ALQ+  +S  LPF
Sbjct: 443 DSGSLVIDSITSGGKTDAPKAQRIFWAVTEGTIAGVLLFVGGEQALNALQAGALSVGLPF 502

Query: 523 SLVMLILVWSLFVGM 537
           +LV+L++ +SLF G+
Sbjct: 503 TLVLLVMTYSLFKGL 517


Lambda     K      H
   0.326    0.139    0.422 

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: 1055
Number of extensions: 77
Number of successful extensions: 5
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: 706
Length of database: 531
Length adjustment: 37
Effective length of query: 669
Effective length of database: 494
Effective search space:   330486
Effective search space used:   330486
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources