GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cycA in Pseudomonas fluorescens FW300-N1B4

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate Pf1N1B4_4976 D-serine/D-alanine/glycine transporter

Query= SwissProt::A0A0H2VDI7
         (470 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4976
           D-serine/D-alanine/glycine transporter
          Length = 473

 Score =  536 bits (1381), Expect = e-157
 Identities = 263/452 (58%), Positives = 337/452 (74%), Gaps = 1/452 (0%)

Query: 9   ADDQAPAEQS-LRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFML 67
           +D     EQ+ L+R L+NRHIQL+A+GGAIGTGLFMGSGK I+L+G SII +YMIIG  +
Sbjct: 3   SDTHEITEQAVLQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFV 62

Query: 68  FFVMRAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQ 127
           +FVMRAMGELLLSNL +KSF+DFA   LGP A +F GW+YW  W V  + D V +  + Q
Sbjct: 63  YFVMRAMGELLLSNLNFKSFADFAGAYLGPRAAFFLGWSYWLSWSVAVVGDAVVVGGFFQ 122

Query: 128 FWFPGLSDWVASLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHF 187
           +WFP +  W+ ++ +++ L  LN+ TVK+FGE+EFWFA+IKI+A+V+LI V ++++A  F
Sbjct: 123 YWFPDVPAWIPAIGMMLTLFALNVLTVKLFGEVEFWFAIIKIIAVVALISVSVLLIASSF 182

Query: 188 QSPTGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPR 247
            SPTGV AS  HL +    FP GL GFFAGFQ+A+F+F G EL+GT AAET+ PEK+LP+
Sbjct: 183 VSPTGVTASLTHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRSPEKTLPK 242

Query: 248 AINSIPIRIIMFYVFSLIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSA 307
           AINSIP+RII+FYV SL+ I++VT W  V P KSPFVELF++ G PAAA ++NFVVLTSA
Sbjct: 243 AINSIPLRIILFYVLSLVCIIAVTSWQQVSPNKSPFVELFLIAGFPAAAGIVNFVVLTSA 302

Query: 308 ASSANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPS 367
           ASSANSGVFS+SRMLFGLA  G AP  F +LSK +VP   L F+   +L GV++L++ P 
Sbjct: 303 ASSANSGVFSSSRMLFGLADLGNAPGIFRRLSKNSVPLISLAFTTFLMLLGVLLLFIIPE 362

Query: 368 VIGAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFV 427
           V+ AFT+++TVSAIL +F W+ IL SY+ YRK RP LH +S YKMP G  M W  +AF  
Sbjct: 363 VMTAFTIVSTVSAILVIFTWSTILASYIAYRKARPDLHAQSRYKMPGGVPMAWFSLAFLA 422

Query: 428 FVLVLLTLEDDTRQALLVTPLWFIALGLGWLF 459
           FVL LL L  DTR AL V P WFI L + + F
Sbjct: 423 FVLCLLALRPDTRLALCVMPAWFIWLAIAYQF 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: 721
Number of extensions: 26
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: 473
Length adjustment: 33
Effective length of query: 437
Effective length of database: 440
Effective search space:   192280
Effective search space used:   192280
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, 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