Alignments for a candidate for betS in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for betS in Pseudomonas stutzeri RCH2

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate GFF3707 Psest_3776 choline/carnitine/betaine transport

Query= SwissProt::G3XCN6
         (706 letters)



>FitnessBrowser__psRCH2:GFF3707
          Length = 657

 Score =  634 bits (1636), Expect = 0.0
 Identities = 321/648 (49%), Positives = 432/648 (66%), Gaps = 14/648 (2%)

Query: 53  VNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFL 112
           +N PVF GS  +I   V   V     A+++F   Q  I++   WLY+L+VA+ L  ++ L
Sbjct: 11  LNAPVFYGSAVIILALVIYSVAFQSHAQTLFGDTQAWIIANVSWLYILAVALILLMVVLL 70

Query: 113 AFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPLTI 172
           AFSRYG++KLGPD SEP++  L+W AMLF+AGMGIGLM+F V EP+ HF SPP  E  T 
Sbjct: 71  AFSRYGDIKLGPDHSEPDYSALTWFAMLFSAGMGIGLMFFGVAEPVMHFLSPPTGEGGTT 130

Query: 173 AAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIGH 232
            A REAM +TFFHWG+HAW+IY++V + LAYF YR+ LPLT+RS LYPL+ E I+GPIGH
Sbjct: 131 LAAREAMKITFFHWGLHAWSIYAIVAMILAYFAYRHGLPLTLRSALYPLIGERIYGPIGH 190

Query: 233 VVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVTG 292
            VDIFAI GT+ G+ATSLG G+ QIN+GLN+L G+P S+ VQ+ L+   T +AT+SVVTG
Sbjct: 191 AVDIFAIIGTVLGVATSLGLGVTQINTGLNHLYGLPISVPVQIGLIIATTLLATVSVVTG 250

Query: 293 VEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEPR 352
           ++KGVR LSE NL LA LL+L VLV GPT  +++ FVQN G YL  +V +TFN+YAYEP 
Sbjct: 251 LDKGVRRLSELNLTLAALLLLMVLVAGPTVFILQTFVQNTGSYLSDIVDKTFNLYAYEPN 310

Query: 353 PWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGNTA 412
            WI  WTLFYW WW++WSPFVG+FIARISRGRT+REFV  VL VP  FT LWMTVFG+TA
Sbjct: 311 DWIGGWTLFYWGWWLAWSPFVGLFIARISRGRTIREFVAGVLLVPTAFTLLWMTVFGDTA 370

Query: 413 IYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGSLVI 472
           I++        L   ++ D S+ALF F E+ P+ A+ S +A+++V +FFVTS+DSG+LV+
Sbjct: 371 IHMILWEHVTSLGDAIEQDSSLALFAFLEHFPFSALISLIAIIMVVVFFVTSADSGALVV 430

Query: 473 DTIASGGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVMLILVWS 532
           D +ASGG+  TP  QRIFW    G VA  LL   GLTALQ+ATI++ALPF++ +L  +W 
Sbjct: 431 DMLASGGKQGTPVWQRIFWAMSMGGVAIALLLADGLTALQTATIASALPFTIALLCSMWG 490

Query: 533 LFVGMRADLAR---TQSPGSLGPRAYPASGVPWQRRLAMTLSTPDRRAVEKFLQASVLPA 589
           L   +R D  +        S  P A P +   WQRRL   +  P R  V +F+   V PA
Sbjct: 491 LLKALRLDATKQGLRYQALSTSPSA-PRTAGGWQRRLRTLMLFPRRAHVVRFITEVVRPA 549

Query: 590 LEAVARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPAFTAYDATVA 649
            E +A E+ ++     +  + E   L   +  +G  DF+Y V+   + +P+F    AT  
Sbjct: 550 YEDIAEEMRKQGYVVEIS-EGEDRRLRFEITHDGEPDFIYEVRPRAYAMPSFV---ATSD 605

Query: 650 DVRYEARTFF------SDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691
           D   E R +F       +G + YD+MG +   +I+D+L Q+E++  F+
Sbjct: 606 DDEREERKYFRAEVHLKEGGQDYDVMGWSREDVISDILGQYEKHMHFL 653


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: 1229
Number of extensions: 55
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: 657
Length adjustment: 39
Effective length of query: 667
Effective length of database: 618
Effective search space:   412206
Effective search space used:   412206
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