Alignments for a candidate for betS in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for betS in Pseudomonas putida KT2440

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate PP_3957 PP_3957 choline/carnitine/betaine transporter BetTC

Query= SwissProt::G3XCN6
         (706 letters)



>FitnessBrowser__Putida:PP_3957
          Length = 657

 Score =  641 bits (1654), Expect = 0.0
 Identities = 326/649 (50%), Positives = 446/649 (68%), Gaps = 10/649 (1%)

Query: 50  RFKVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSM 109
           R  +N PVF  S  ++ L V       + A+++F  +Q  I++   W Y+L VA+ L S+
Sbjct: 8   RSTLNPPVFYTSAILVFLLVLYATAFQEHAQTLFEQVQRWIITNASWFYILVVALVLISV 67

Query: 110 LFLAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEP 169
           +FLA SRYG++KLGPD SEP++R  SW AMLF+AGMGIGLM+F V EP+ HF++PP  +P
Sbjct: 68  VFLAVSRYGDIKLGPDHSEPDYRKSSWFAMLFSAGMGIGLMFFGVAEPVMHFSTPPVGDP 127

Query: 170 LTIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGP 229
            T+AA REAM +TFFHWG+HAWAIY++V L LAYF +R  LPLT+RS LYPL+ E I+GP
Sbjct: 128 GTVAAAREAMKITFFHWGLHAWAIYAIVALILAYFSFRNGLPLTLRSALYPLIGERIYGP 187

Query: 230 IGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISV 289
           IGH VD+FAI GT+FG+ATSLG+G+LQINSG +++ G+P +  VQ++L+T   A+AT+SV
Sbjct: 188 IGHAVDVFAILGTVFGVATSLGYGVLQINSGFHHVFGLPVNTTVQVILITATCALATLSV 247

Query: 290 VTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAY 349
            +G++KG+RILSE NL LAV+LMLFVL++GPT  L++ +VQN G YL  +V +TFN+YAY
Sbjct: 248 ASGLDKGIRILSELNLSLAVILMLFVLLLGPTVFLLQTYVQNTGAYLSDIVNKTFNLYAY 307

Query: 350 EPRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFG 409
           EP  WI  WTL YW WW+SWSPFVG+FIARISRGRT+REFV  VLFVPA FT LWMTVFG
Sbjct: 308 EPTDWIGGWTLLYWGWWLSWSPFVGLFIARISRGRTIREFVCGVLFVPAGFTLLWMTVFG 367

Query: 410 NTAIYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGS 469
           ++AI++       +LA  V  D S+ALF F E+ P+ ++ S +AVL+V +FFVTS+DSG+
Sbjct: 368 DSAIHMILNDGVKDLAAVVSEDSSLALFAFLEHFPFSSIISLVAVLMVVVFFVTSADSGA 427

Query: 470 LVIDTIASGGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVMLIL 529
           LV+D +AS G+  +P  QRIFW    G VA  LL   GL ALQ+ATI++ALPF++++L+ 
Sbjct: 428 LVVDMLASSGQGHSPLWQRIFWSVCIGAVAIALLLANGLKALQTATIASALPFAVILLVA 487

Query: 530 VWSLFVGMRADLAR--TQSPGSLGPR--AYPASGVPWQRRLAMTLSTPDRRAVEKFLQAS 585
           +W LF  +  D  R   ++    GPR   +P  G  WQRRL      P R  V +F+   
Sbjct: 488 IWGLFKALSLDATRRGLRNQALPGPRHTRHPHGG--WQRRLRNIALMPRRVHVTRFIAEV 545

Query: 586 VLPALEAVARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPAFTAYD 645
           V PA E VA+EL ++    SV  + + G ++L +   G   F+Y V+      P+F   D
Sbjct: 546 VRPACEEVAQELRKQGYEVSV-NERDDGRVSLELSHAGEGRFLYEVRPRAFNTPSFVMRD 604

Query: 646 A-TVADVR--YEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691
               AD R  + A     +G + YDIMG + + +I D+L Q+ER+  ++
Sbjct: 605 TEDGADSRKYFRAEVHLREGGQDYDIMGWSRDDVIGDILDQYERHLHYL 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: 1191
Number of extensions: 50
Number of successful extensions: 3
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