GapMind for catabolism of small carbon sources

 

Alignments for a candidate for RR42_RS28305 in Pseudomonas putida KT2440

Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate PP_4840 PP_4840 D-alanine, beta-alanine, D-serine, glycine permease

Query= uniprot:A0A0C4YRF7
         (472 letters)



>FitnessBrowser__Putida:PP_4840
          Length = 468

 Score =  451 bits (1161), Expect = e-131
 Identities = 217/450 (48%), Positives = 313/450 (69%), Gaps = 4/450 (0%)

Query: 15  EEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRAL 74
           +E  L R L +RHIQ+IAIGGAIG GLF+G+G+ I++AGP ++  Y I G  +FF+MRA+
Sbjct: 10  DEPHLQRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAM 69

Query: 75  GELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVP 134
           GELLL      SF  ++ + +GP+AG+ TGW+YWF WVVTG+A++ A+A Y  +WFPD+P
Sbjct: 70  GELLLSNLNYKSFIDFSADLLGPWAGYFTGWTYWFCWVVTGIADVVAIAAYTQFWFPDLP 129

Query: 135 QWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVT-PLGPT 193
           QWIPAL  + +L  +N V V +FGELEFWFAL+K+V I+ ++  GL ++  G T P G T
Sbjct: 130 QWIPALTCVGLLLSLNLVTVKMFGELEFWFALVKIVAILGLVATGLYMVITGFTSPSGRT 189

Query: 194 ASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVW 253
           A  +NLW  GG  P G +G     QI +FA+ G+EL+G TA EA+NPE+ LP A N +  
Sbjct: 190 AQLANLWNDGGMFPHGLMGFFAGFQIAVFAFVGIELVGTTAAEAKNPERTLPRAINSIPI 249

Query: 254 RILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSG 313
           RI++FYV ALI +MA+ PW ++ PG SPFV +F   G+P AA+I+N VV+T+AASS NSG
Sbjct: 250 RIIVFYVLALIAIMAVTPWRDVVPGKSPFVELFVLAGLPAAASIINFVVLTSAASSANSG 309

Query: 314 IFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPE--QVFVW 371
           +FST RMLY L+Q G AP+AF ++SS+ VP+  + FS   + +G +L Y+VP   + F  
Sbjct: 310 VFSTSRMLYGLSQEGDAPKAFEKLSSRSVPANGLYFSCTCLLLGAVLIYLVPNVVEAFTL 369

Query: 372 VTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLL 431
           VT++S V  ++ W++I++++L YRK  AA   +A  ++MPG  +  ++ ++F   + VLL
Sbjct: 370 VTTVSAVLFMFVWTLILLSYLKYRKDRAALH-QASNYKMPGGRFMCYVCLSFFAFILVLL 428

Query: 432 SLDPGTRVALYVAPVWFALLGIGYRFTKSR 461
           SL+  TR AL V P+WF +L + Y+  +SR
Sbjct: 429 SLEADTRSALVVTPIWFVVLAVTYQLVRSR 458


Lambda     K      H
   0.328    0.142    0.445 

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: 698
Number of extensions: 28
Number of successful extensions: 4
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: 472
Length of database: 468
Length adjustment: 33
Effective length of query: 439
Effective length of database: 435
Effective search space:   190965
Effective search space used:   190965
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 (21.8 bits)
S2: 51 (24.3 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:

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:

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:

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:

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