GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Putida:PP_4840 PP_4840 D-alanine, beta-alanine,
           D-serine, glycine permease
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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