Alignments for a candidate for betS in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for betS in Pseudomonas litoralis 2SM5

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate WP_090271580.1 BLU11_RS00755 BCCT family transporter

Query= SwissProt::G3XCN6
         (706 letters)



>NCBI__GCF_900105005.1:WP_090271580.1
          Length = 685

 Score =  568 bits (1463), Expect = e-166
 Identities = 289/643 (44%), Positives = 416/643 (64%), Gaps = 6/643 (0%)

Query: 55  LPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFLAF 114
           LPVF+ S   I L V      P+ A  +FS + + I + FGW Y+LSVA+FL  ++ +A 
Sbjct: 16  LPVFIPSFFFILLLVISTATQPELAGELFSSVLSYITTTFGWFYMLSVAIFLVFIVIVAM 75

Query: 115 SRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPE-AEPLTIA 173
           S++G +KLGPD +EP++ + +W AMLF+AG GI L++F V EP+ H+A PP+ AE LT+ 
Sbjct: 76  SKWGHIKLGPDHAEPQYSFPAWFAMLFSAGYGIALLFFGVAEPVLHYAEPPQGAEGLTVD 135

Query: 174 AQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIGHV 233
           A ++AM + FFHWG H WAIY + GL LAYF +R+ LPL++RS LYPL+ + I+GPIGH 
Sbjct: 136 AAKQAMQIAFFHWGFHIWAIYGLTGLVLAYFSFRHGLPLSIRSALYPLIGDRIYGPIGHA 195

Query: 234 VDIFAICGTMFGLATSLGFGILQINSGLNYLL-GIPQSIYVQLLLVTVVTAIATISVVTG 292
           VD FAI GTMFG+AT+LG  + QIN+GLNYL   IP  I VQ+  +  +T +   SV+ G
Sbjct: 196 VDTFAILGTMFGIATTLGLSVAQINAGLNYLWPSIPIGIGVQVGTIAFITFLTMGSVIAG 255

Query: 293 VEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEPR 352
           ++KG++ LS  N+ +A  LMLFV   GPT  ++  F+QN G YL+++V RTFN+ AY   
Sbjct: 256 MDKGIKNLSMLNMIVATSLMLFVFFAGPTIFILEAFLQNTGSYLNNIVERTFNLQAYSRS 315

Query: 353 PWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGNTA 412
            WI +WTLF + W I+W+PFVG+FIA+ISRGRT+R+FV  V+ VP +FTF W +VFG+TA
Sbjct: 316 DWIGNWTLFIFGWTIAWAPFVGLFIAKISRGRTIRQFVFGVMLVPTIFTFFWFSVFGDTA 375

Query: 413 IYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGSLVI 472
           +++        L   V+AD ++ALF+ FE LP  A+ ST+ V+L+++FF+TS+DSG+LV+
Sbjct: 376 LHLIINQGYSVLIDQVQADNAIALFKLFEQLPMTAIISTITVILITLFFITSADSGALVV 435

Query: 473 DTIASGGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVMLILVWS 532
           D++ASGG   TPA QR FW  LSG++A+VLL  GGL ALQS  +++ALPF+++MLI    
Sbjct: 436 DSLASGGALVTPAWQRGFWAILSGVLASVLLVAGGLKALQSMAVASALPFAVIMLISAVG 495

Query: 533 LFVGMRADLARTQSPGSLGPRAYPASGVPWQRRLAMTLSTPDRRAVEKFLQASVLPALEA 592
           ++  +  +    Q     G          W++RLA  ++ P +  VE F++ + L A+  
Sbjct: 496 MWRALTIESHHQQVSVGPGNHTTGRGAALWKKRLAGIVNYPAKDEVEMFIKDTALTAMIR 555

Query: 593 VARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPAFT--AYDATVAD 650
           VA+ L  +S PA V  D E     L +      DF+Y +++ ++  PAF     + T  D
Sbjct: 556 VAKGLQAQSWPAEVHYDEEHKRAYLEIITPDQLDFLYEIRLRDYLRPAFAHPEVEETADD 615

Query: 651 --VRYEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691
               Y A  F   G + YDI G    +II D+L  FE+Y  F+
Sbjct: 616 DSFYYRAEVFLRRGGQAYDIYGYDQQEIIGDILDHFEKYLHFL 658


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: 1344
Number of extensions: 71
Number of successful extensions: 6
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: 685
Length adjustment: 39
Effective length of query: 667
Effective length of database: 646
Effective search space:   430882
Effective search space used:   430882
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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 2024 update 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