GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Pseudomonas simiae WCS417

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate GFF2849 PS417_14545 amino acid transporter

Query= SwissProt::A0A0H2VDI7
         (470 letters)



>FitnessBrowser__WCS417:GFF2849
          Length = 465

 Score =  534 bits (1375), Expect = e-156
 Identities = 261/442 (59%), Positives = 335/442 (75%)

Query: 18  SLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGEL 77
           +L+R L+NRHIQL+A+GGAIGTGLFMGSGK I+L+G SII +YMIIG  ++FVMRAMGEL
Sbjct: 13  ALQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFVYFVMRAMGEL 72

Query: 78  LLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPGLSDWV 137
           LLSNL +KSF+DFA   LGP A +F GW+YW  W V  + D V +  + Q+WFP +  W+
Sbjct: 73  LLSNLNFKSFADFAGAYLGPRAAFFLGWSYWLSWSVAVIGDAVVVGGFFQYWFPHVPAWM 132

Query: 138 ASLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEASF 197
            ++ +++ L  LN+ TV++FGE+EFWFA+IK++A+++LI V  V++A  F SPTGV ASF
Sbjct: 133 PAVGMLLTLFALNVLTVRLFGEVEFWFAIIKLIAVLTLIGVSGVLIASSFVSPTGVTASF 192

Query: 198 AHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIRII 257
            HL +    FP GL GFFAGFQ+A+F+F G EL+GT AAET+ PEK+LP+AINSIP+RII
Sbjct: 193 THLLDPQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRAPEKTLPKAINSIPLRII 252

Query: 258 MFYVFSLIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGVFS 317
           +FYV +L  I++VT W  V P KSPFVELF++ G PAAA ++NFVVLTSAASSANSGVFS
Sbjct: 253 LFYVLALACIIAVTSWQHVSPSKSPFVELFLVAGFPAAAGIVNFVVLTSAASSANSGVFS 312

Query: 318 TSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMITT 377
            SRMLFGLA  G AP  F +LSK +VP   L F+ + +L G+V+L+V P V+ AFT+++T
Sbjct: 313 ASRMLFGLADLGDAPGIFRRLSKSSVPFISLAFTTLLMLLGLVLLFVVPEVMTAFTIVST 372

Query: 378 VSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVLVLLTLED 437
           VSAIL +F W+ IL SY+ YRK+RP LH KS+YKMP G LM W  +AF  FVL LL L  
Sbjct: 373 VSAILVIFTWSTILASYIAYRKKRPDLHAKSLYKMPGGVLMAWFSLAFLAFVLGLLALRP 432

Query: 438 DTRQALLVTPLWFIALGLGWLF 459
           DTR AL V P WFI L + + F
Sbjct: 433 DTRLALCVMPAWFIWLWIAYPF 454


Lambda     K      H
   0.329    0.141    0.441 

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: 768
Number of extensions: 35
Number of successful extensions: 1
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: 470
Length of database: 465
Length adjustment: 33
Effective length of query: 437
Effective length of database: 432
Effective search space:   188784
Effective search space used:   188784
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