Alignments for a candidate for Psest_0084 in Rhodopseudomonas palustris CGA009

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Rhodopseudomonas palustris CGA009

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate WP_011160041.1 TX73_RS23040 C4-dicarboxylate ABC transporter

Query= reanno::psRCH2:GFF84
         (674 letters)



>NCBI__GCF_000195775.1:WP_011160041.1
          Length = 706

 Score =  712 bits (1839), Expect = 0.0
 Identities = 370/668 (55%), Positives = 476/668 (71%), Gaps = 12/668 (1%)

Query: 11  PSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYPARGNGKPF-Q 69
           P  W    + VA+ F+ +Q+V AA++ + SQV+R  HVGFLLLL F           F +
Sbjct: 32  PRGWRYLAYAVAIAFASFQLVIAAWNVLPSQVVRGVHVGFLLLLTFGLIGNFTARTDFGR 91

Query: 70  PVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARRVMGIALPI 129
            +AWL G  GF    YQW F ADLIQR GD T  D+ VG  L VL+FE  RR+MG ALPI
Sbjct: 92  AIAWLTGAVGFFCGLYQWIFYADLIQRDGDPTHLDLAVGTLLAVLIFEGTRRLMGPALPI 151

Query: 130 ICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYIFLFILFGS 189
           +C + L Y   G+YLP    HRGY  DQ++  LSFGTEG YG P YVSATYIFLFILFGS
Sbjct: 152 MCGVCLLYWFFGQYLPAPFNHRGYDFDQVITHLSFGTEGFYGVPIYVSATYIFLFILFGS 211

Query: 190 FLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTGQFTIPLMK 249
           FLE+AGMI+LFTD ++GLFG   GGPAKV+V +S +MGTI+GSGVANVVT GQFTIPLM 
Sbjct: 212 FLERAGMIQLFTDVSLGLFGRSRGGPAKVAVFASGMMGTISGSGVANVVTVGQFTIPLMI 271

Query: 250 RFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPALLYFGSV 309
           +FGYR AFA GVEAT+SMG QIMPPVMGAVAFIMAET+ V +  I KAA+IPA+LYF S 
Sbjct: 272 KFGYRRAFAAGVEATASMGGQIMPPVMGAVAFIMAETLGVDYAVIVKAAVIPAILYFASA 331

Query: 310 FWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTPMFAGTIGLA 369
           FWMVHLEA + GL G+ K E PSA  A  +RWYL++PL  LV++LF G TP++AG++GLA
Sbjct: 332 FWMVHLEAGKHGLVGMKKSEIPSAWRAAVDRWYLILPLAALVFMLFEGFTPLYAGSMGLA 391

Query: 370 LTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGV--IFGVIAALVAVCWFIK 427
           LT  +ILG++I+   SN  LR  FWI L L+       G+ +  I  ++AALVA+    +
Sbjct: 392 LTVALILGASIVHGFSNTVLRYVFWIGLALVVGAASHNGLDIMRIVVIVAALVAIAAITR 451

Query: 428 GGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAVGENNLFL 487
           GGR TL  C  +L + A+ A+ VG+ACA+VG IIG+++ TGV + F  +++ +GE++LFL
Sbjct: 452 GGRATLRACRDSLADSAKSALTVGMACAIVGTIIGMMTQTGVGTVFGTWVIGLGEHSLFL 511

Query: 488 SLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIMADLTPPV 547
           +L++TML  ++LG GIPTIP YIIT+++AAPAL  LGVPLIVSHMF FY+GIMADL+PPV
Sbjct: 512 ALVMTMLLSILLGTGIPTIPTYIITAALAAPALAKLGVPLIVSHMFAFYYGIMADLSPPV 571

Query: 548 ALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGD--------WGAT 599
           ALA  AAAPIA+E   KI   A+RIA+AG+++PF+AVY+PALM+Q GD        +GA 
Sbjct: 572 ALAALAAAPIARENPDKIGWEAMRIALAGYVIPFIAVYSPALMLQPGDPMAAELGFYGAV 631

Query: 600 LYMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFL 659
           +Y  FKA  A+GL+G V  G+L   M + E+++AFAA+  ++     SD IGF + A+ +
Sbjct: 632 VYATFKALIAIGLFGMVSIGFLYTRMTVIERIVAFAASICLLGEFAYSDYIGFLITAV-V 690

Query: 660 IQHIWRAR 667
           +   WR R
Sbjct: 691 VAWQWRQR 698


Lambda     K      H
   0.330    0.143    0.445 

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: 1545
Number of extensions: 73
Number of successful extensions: 6
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: 674
Length of database: 706
Length adjustment: 39
Effective length of query: 635
Effective length of database: 667
Effective search space:   423545
Effective search space used:   423545
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
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
the source code
instructions for running GapMind on your computer

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