Alignments for a candidate for betS in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for betS in Shewanella sp. ANA-3

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate 7025568 Shewana3_2719 choline/carnitine/betaine transporter (RefSeq)

Query= SwissProt::G3XCN6
         (706 letters)



>FitnessBrowser__ANA3:7025568
          Length = 658

 Score =  612 bits (1577), Expect = e-179
 Identities = 308/643 (47%), Positives = 426/643 (66%), Gaps = 6/643 (0%)

Query: 53  VNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFL 112
           +N PVF  SV  I L V I  I P  A   F  MQ+ + +  GWLY+L VA+FL  ++F+
Sbjct: 7   INPPVFYSSVFFITLMVMICAIWPTEANHFFKSMQSWLEAKAGWLYILGVAIFLIFIIFV 66

Query: 113 AFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPLTI 172
             SR+G++KLGPD + P++ Y SWIAMLF+AGMGIGLM+F V EP+ H+ +PP+A P ++
Sbjct: 67  MVSRFGDIKLGPDHAVPDYSYKSWIAMLFSAGMGIGLMFFGVAEPVMHYLAPPDATPESL 126

Query: 173 AAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIGH 232
           AA +EAM +TFFHWG+HAWAIY VV LSLAYF YR+ LPL  RS LYPL+ E IHGPIGH
Sbjct: 127 AAAKEAMKITFFHWGIHAWAIYGVVALSLAYFAYRHKLPLLPRSALYPLIGERIHGPIGH 186

Query: 233 VVDIFAICGTMFGLATSLGFGILQINSGLNYLL-GIPQSIYVQLLLVTVVTAIATISVVT 291
            VD FA+ GTMFG+ATSLGFG+LQ+NSGL+YL   +P +  VQ+ L+  +T +AT+SV +
Sbjct: 187 CVDTFAVLGTMFGVATSLGFGVLQVNSGLSYLFEQLPNNTTVQVSLIIGITLLATLSVFS 246

Query: 292 GVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEP 351
           G++KGV+ LSE NL LA++L+L VL++GPT  L++ FVQN G YL  +V +TFN+YAY+ 
Sbjct: 247 GLDKGVKRLSELNLGLALILLLIVLILGPTVMLLQAFVQNTGSYLSDIVNKTFNLYAYQH 306

Query: 352 R-PWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGN 410
           +  W+  WTL YW WWISWSPFVG FIAR+SRGRT+REF+  +LFVP+  TFLWMTVFGN
Sbjct: 307 KEDWLGGWTLLYWGWWISWSPFVGTFIARVSRGRTIREFLVGILFVPSALTFLWMTVFGN 366

Query: 411 TAIYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGSL 470
           +AI          L+  V  ++ VALF FFE++P+P + S + + LV  FFVTSSDSGSL
Sbjct: 367 SAIDAIMNQGATYLSEAVNTNVPVALFVFFEHMPFPHLLSGIGICLVVTFFVTSSDSGSL 426

Query: 471 VIDTIASGGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVMLILV 530
           VID + SGG+   P  QR+FW  L G+VA+VLL  GGL ALQ+A I++A+PF  VML++ 
Sbjct: 427 VIDNLTSGGDNNAPVWQRVFWALLQGVVASVLLLAGGLQALQTAAIASAMPFLCVMLLMC 486

Query: 531 WSLFVGMRADLARTQSPG-SLGPRAYPASGVPWQRRLAMTLSTPDRRAVEKFLQASVLPA 589
             L+  ++ D  +  S         Y  + + W+ R+ + +S P       FL     PA
Sbjct: 487 LGLYKALKDDWLKINSVQLHTTSVQYAKTNISWEERIEVLVSHPTEDEARIFLNNVATPA 546

Query: 590 LEAVARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPAFTAYDATVA 649
           L  V ++   +   A +  +   G + L +  E ++ FVYGV+M   ++      +    
Sbjct: 547 LSKVCQQFMSKGLTADL--EYLDGKVRLVISNEAYQPFVYGVRMRCFEIVNPVGEELEQG 604

Query: 650 -DVRYEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691
            +  Y A  +   G + YD+MG  + Q++ DV+ Q+E+Y  ++
Sbjct: 605 NNWYYRAEVYLEQGGQHYDVMGYTEEQLLADVVTQYEKYLHYL 647


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: 1215
Number of extensions: 64
Number of successful extensions: 7
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: 658
Length adjustment: 39
Effective length of query: 667
Effective length of database: 619
Effective search space:   412873
Effective search space used:   412873
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 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:

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