Alignments for a candidate for Psest_0084 in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Sulfuritalea hydrogenivorans DSM 22779

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate WP_084207458.1 SUTH_RS16130 TRAP transporter permease

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



>NCBI__GCF_000828635.1:WP_084207458.1
          Length = 703

 Score =  813 bits (2099), Expect = 0.0
 Identities = 420/673 (62%), Positives = 511/673 (75%), Gaps = 13/673 (1%)

Query: 14  WPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYPARGNGKPFQPVA- 72
           W   L  +AL FS YQ++ AAFHP+SS V+R+ HVGFLL + F+ YPA  N      V  
Sbjct: 28  WLTVLTGLALTFSTYQLIVAAFHPLSSLVIRSLHVGFLLCITFILYPAFKNSGRLSKVGA 87

Query: 73  --WLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARRVMGIALPII 130
               L     A   Y W FEA+LIQRSGD +T D+ VG  L++L FEAARR++G+ALPI+
Sbjct: 88  GDTALAFGALALSTYHWAFEAELIQRSGDPSTVDLFVGTALVILTFEAARRILGLALPIV 147

Query: 131 CALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYIFLFILFGSF 190
           C LFL YG+ G  LPG L HR Y  DQI+NQL+ GTEG++G PT VSATYIFLFILFGSF
Sbjct: 148 CGLFLLYGVFGHLLPGSLGHREYGFDQIINQLALGTEGIFGIPTLVSATYIFLFILFGSF 207

Query: 191 LEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTGQFTIPLMKR 250
           LE AGMI LF   A+G  GH  GGPAKVSV+SS LMGTI+GSGVANV+TTGQFTIPLMK+
Sbjct: 208 LEHAGMINLFNSLALGFVGHTKGGPAKVSVISSGLMGTISGSGVANVLTTGQFTIPLMKK 267

Query: 251 FGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPALLYFGSVF 310
           FGY   FAG VEATSSMG QIMPPVMGAVAFIMAE INVP+ +I +AA IPA+LY+ + F
Sbjct: 268 FGYSGIFAGAVEATSSMGGQIMPPVMGAVAFIMAENINVPYADIVQAAAIPAILYYLTAF 327

Query: 311 WMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTPMFAGTIGLAL 370
           WMVHLEA R  L GLPK ECP+   A+++ WYLL+PLVVLVW LF+G TPMFAG IGL L
Sbjct: 328 WMVHLEAGRKNLVGLPKAECPNPWHAMRDNWYLLLPLVVLVWTLFNGFTPMFAGMIGLVL 387

Query: 371 TAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQ----LGIGVIFGVIAALVAVCWFI 426
           TA++ILG+AI  +VS+ A R  FW ALGL  A F +     GI  +  +IAALVA  + +
Sbjct: 388 TAVLILGAAIAARVSSAAFRYVFWFALGLAAAVFVKNMETWGIFPLLALIAALVAQTFAL 447

Query: 427 KGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAVGENNLF 486
           KGG  TL +   +LVEGA+ A+PVG+ACA+VGVIIGV++LTG AS+FAG+IL+VGE +LF
Sbjct: 448 KGGMKTLHLLKMSLVEGAQQALPVGVACAIVGVIIGVLTLTGAASSFAGFILSVGEKSLF 507

Query: 487 LSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIMADLTPP 546
           LSL+LTML CLVLGMGIPTIPNYIITSSIAAPALL LGVPLIVSHMFVFYFGIMADLTPP
Sbjct: 508 LSLVLTMLVCLVLGMGIPTIPNYIITSSIAAPALLKLGVPLIVSHMFVFYFGIMADLTPP 567

Query: 547 VALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDW--GATLYMLF 604
           VALA FAAA IAKE  +KI   A++IAIAGF++P+MAVY PALM+Q GDW   A  Y++F
Sbjct: 568 VALAAFAAASIAKESAMKIGFKAVQIAIAGFVIPYMAVYTPALMLQ-GDWTFAAVAYIVF 626

Query: 605 KAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFLIQHIW 664
           KA  ++ LWGA   G++   + + E++ A AAA  +V A+P++DEIGF + A+F++ H+ 
Sbjct: 627 KAVVSIMLWGAAAIGFMFASLNMAERIFAAAAAFLLVAAIPLTDEIGFVMSAVFVVWHLL 686

Query: 665 RARRA---EPATA 674
           R+R+A    PA+A
Sbjct: 687 RSRQAAARRPASA 699


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: 1479
Number of extensions: 82
Number of successful extensions: 5
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: 703
Length adjustment: 39
Effective length of query: 635
Effective length of database: 664
Effective search space:   421640
Effective search space used:   421640
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 Apr 09 2024. 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:

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