GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Pseudomonas fluorescens FW300-N2C3

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate AO356_29455 AO356_29455 amino acid transporter

Query= SwissProt::P0AAE0
         (470 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_29455
          Length = 484

 Score =  532 bits (1371), Expect = e-156
 Identities = 257/442 (58%), Positives = 336/442 (76%)

Query: 16  EQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMG 75
           + +L+R L+NRHIQL+A+GGAIGTGLFMGSGK I+L+G SII +YMIIG  ++FVMRAMG
Sbjct: 11  QPALQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFVYFVMRAMG 70

Query: 76  ELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSD 135
           E+LLSNL +K+F+DFA   LGP A +F GW+YW  W V  + D V +  + Q+WFPD+  
Sbjct: 71  EMLLSNLNFKTFADFAGAYLGPRAAFFLGWSYWLSWSVAVIGDAVVVGGFFQYWFPDVPA 130

Query: 136 WVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEA 195
           W+ ++ +++ L  LN+ TV++FGE+EFWFA+IKI+A+V+LI V LV++A  F SP+GV A
Sbjct: 131 WIPAIGMLMTLFALNVLTVRLFGEIEFWFAIIKIIAVVTLIGVSLVLIASSFVSPSGVTA 190

Query: 196 SFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIR 255
           S  HL +    FP GL GFFAGFQ+A+F+F G EL+GT AAET++PEK+LP+AINSIP+R
Sbjct: 191 SLNHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRNPEKTLPKAINSIPLR 250

Query: 256 IIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGV 315
           II+FYV AL  I++VT W  V P KSPFVELF++ G PAAA ++NFVVLTSAASSANSGV
Sbjct: 251 IILFYVLALACIIAVTSWQQVSPSKSPFVELFLVAGFPAAAGIVNFVVLTSAASSANSGV 310

Query: 316 FSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMI 375
           FS+SRMLFGLA +  AP  F +LS  +VP   L F+ + +L GV++L++ P V+ AFT++
Sbjct: 311 FSSSRMLFGLANQDNAPGIFRRLSGNSVPLLSLAFTTLLMLVGVLLLFIVPEVMTAFTIV 370

Query: 376 TTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVVVLLTL 435
           +TVSAIL +F W+ IL SY+ YRK+RP LH KS YKMP G  M W  +AF  FV+ LL L
Sbjct: 371 STVSAILVIFTWSTILASYIAYRKKRPELHAKSAYKMPGGVPMAWFSLAFLGFVLCLLAL 430

Query: 436 EDDTRQALLVTPLWFIALGLGW 457
             DTR ALLV P WFI L + +
Sbjct: 431 RPDTRIALLVMPGWFIWLAIAY 452


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: 733
Number of extensions: 33
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: 484
Length adjustment: 33
Effective length of query: 437
Effective length of database: 451
Effective search space:   197087
Effective search space used:   197087
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