Aligments for a candidate for cycA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments 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::P0AAE0
         (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  LLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDWV 137
           LLSNL +KSF+DFA   LGP A +F GW+YW  W V  + D V +  + Q+WFP +  W+
Sbjct: 73  LLSNLNFKSFADFAGAYLGPRAAFFLGWSYWLSWSVAVIGDAVVVGGFFQYWFPHVPAWM 132

Query: 138 ASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEASF 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 MFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGVFS 317
           +FYV AL  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 VSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVVVLLTLED 437
           VSAIL +F W+ IL SY+ YRK+RP LH KS+YKMP G LM W  +AF  FV+ 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    0.440 

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: 758
Number of extensions: 34
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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Steps (tab-delimited)
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Protein sequences (fasta format)
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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, 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

GapMind for catabolism of small carbon sources