GapMind for catabolism of small carbon sources

 

Alignments 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::P0AAE0
         (470 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4976
          Length = 473

 Score =  536 bits (1381), Expect = e-157
 Identities = 262/452 (57%), Positives = 338/452 (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 FWFPDLSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHF 187
           +WFPD+  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 AINSIPIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSA 307
           AINSIP+RII+FYV +L+ 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 FVVVLLTLEDDTRQALLVTPLWFIALGLGWLF 459
           FV+ LL L  DTR AL V P WFI L + + F
Sbjct: 423 FVLCLLALRPDTRLALCVMPAWFIWLAIAYQF 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: 713
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 (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