Alignments for a candidate for Psest_0084 in Desulfatibacillum aliphaticivorans DSM 15576

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Desulfatibacillum aliphaticivorans DSM 15576

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate WP_028316487.1 G491_RS0125035 DUF3394 domain-containing protein

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



>NCBI__GCF_000429905.1:WP_028316487.1
          Length = 683

 Score =  351 bits (901), Expect = e-101
 Identities = 211/567 (37%), Positives = 318/567 (56%), Gaps = 57/567 (10%)

Query: 44  RAGHVGFLLLLVFLCYPARGNGK------------PFQPVAWLLGLAGFATFFYQWYFEA 91
           RA H+ F + L+FL  P     +            P    A L  +A  A+ +    ++ 
Sbjct: 59  RAFHLAFAIALLFLLTPLMRKARKGMEYFFVTDRIPLMDYA-LAVIAVIASLYIVIDYDG 117

Query: 92  DLIQRSGDMTTADMVVGLTLIVLVFEAARRVMGIALPIICALFLAYGLLGEYLPGDLAHR 151
            L  R+G   T D+  G+ L+V++ EAARRV+G AL II  +F  Y  LG Y+P  LA +
Sbjct: 118 -LAYRAGMPITRDIAFGVVLVVVLLEAARRVIGPALSIIAIVFTVYAFLGPYMPDFLAFK 176

Query: 152 GYYLDQIVNQLSFGTEGLYGTPTYVSATYIFLFILFGSFLEQAGMIKLFTDFAMGLFGHK 211
           G  L +  + +S  TEG+YG P  VSA+ ++LF+L G+ L++AG  + FTD A+   G  
Sbjct: 177 GVSLRKYCSNISLSTEGIYGIPLGVSASIVYLFVLLGALLDKAGAGQFFTDLALSFLGKY 236

Query: 212 LGGPAKVSVVSSALMGTITGSGVANVVTTGQFTIPLMKRFGYRPAFAGGVEATSSMGSQI 271
            GGPAK +VV+S   G ++GS +AN+VTTG FTIPLMK+ GY    A  VE  SS   Q+
Sbjct: 237 KGGPAKAAVVASGATGLVSGSSIANIVTTGPFTIPLMKKVGYPAKKAAAVEVASSTDGQL 296

Query: 272 MPPVMGAVAFIMAETINVPFVEIAKAALIPALLYFGSVFWMVHLEAKRAGLKGLPKDECP 331
           MPP+MGA AFI+AE +NVP++E+ KAA IPA   +  +F + HLEA + G+ GL K E P
Sbjct: 297 MPPIMGAAAFIIAEYVNVPYIEVVKAAAIPAFASYFGLFCITHLEASKLGISGLAKHEVP 356

Query: 332 SAMAAVKERWYLLIPLVVLVW-LLFSGRTPMFAGTIGLALTAIVILGSAIILKVSNFALR 390
                +K   + L+PL VL++ L+    +P  A     A  AI+IL   I  +     LR
Sbjct: 357 VFFQTLKGGLHYLLPLGVLLYELIILRHSPEMA-----AFRAILILFVVIFYQ----ELR 407

Query: 391 IAFWIALGLLCAGFFQLGIGVIFGVIAALVAVCWFIKGGRDTLVICLHALVEGARHAVPV 450
            +F              GIG                +G  D++ I    +++G+++ +PV
Sbjct: 408 RSFKAG----------TGIG----------------QGFMDSIRIIGMGMIQGSKNMMPV 441

Query: 451 GIACALVGVIIGVVSLTGVASTFAGYILAVGENNLFLSLLLTMLTCLVLGMGIPTIPNYI 510
            +ACA  G+I+GVV++ G+    A  +  + + N++L LL+T +  L+LGMG+PT   YI
Sbjct: 442 ALACAAAGIIVGVVNM-GIGGMVAQIVETLSQGNIYLLLLITAIASLLLGMGLPTTATYI 500

Query: 511 ITSSIAAPALLDLG------VPLIVSHMFVFYFGIMADLTPPVALACFAAAPIAKERGLK 564
           + +S+ AP ++ +G      +PLI +H+F FYFGI+AD TPPV LA +AA+ IA    + 
Sbjct: 501 VMASLTAPIIVQVGGNFGFVLPLIAAHLFCFYFGILADDTPPVGLAAYAASAIADSDPIP 560

Query: 565 ISMWAIRIAIAGFIVPFMAVYNPALMM 591
             +   +  I   ++ F+ V+NP L++
Sbjct: 561 TGIQGFKYDIRTSVIAFLFVFNPDLLL 587


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: 1253
Number of extensions: 73
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: 683
Length adjustment: 39
Effective length of query: 635
Effective length of database: 644
Effective search space:   408940
Effective search space used:   408940
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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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