Alignments for a candidate for Psest_0084 in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Halomonas desiderata SP1

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate WP_086508325.1 BZY95_RS01940 permease

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



>NCBI__GCF_002151265.1:WP_086508325.1
          Length = 673

 Score =  433 bits (1113), Expect = e-125
 Identities = 250/660 (37%), Positives = 384/660 (58%), Gaps = 50/660 (7%)

Query: 21  VALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYPARGNGKPFQPVAWLLGLAGF 80
           VA+  S++Q+ +A   P+     R+ H+  +++L FL +P  G  +    + WL+  A F
Sbjct: 29  VAVGLSLFQLYSAGIQPLGLFYQRSVHLMLIMMLAFLIFPVFGPNRKRGVLGWLIDAAFF 88

Query: 81  A----TFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARRVMGIALPIICALFLA 136
           A    T  Y   +  ++I+R+G  +  D++VG   +V V EA+RR +G+ + II A+ + 
Sbjct: 89  AGALITGGYMVLYLDEIIRRAGFWSQTDIIVGCIAVVTVLEASRRAVGLGMTIIGAIAIL 148

Query: 137 YGL---------LGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYIFLFILF 187
           Y           LG+++PG L HRGY LD++V QL  G EG++G P  V+AT+IF+F+LF
Sbjct: 149 YAFAGPRGELPWLGQFMPGILEHRGYNLDRVVGQLYLGQEGIFGLPLGVAATFIFVFVLF 208

Query: 188 GSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTGQFTIPL 247
           G+FLE  G  K F D A    G + GGPAK +V++SA MG+I+GS +ANVVTTG FTIPL
Sbjct: 209 GAFLESTGAGKFFIDMAYAATGRQRGGPAKAAVIASAGMGSISGSAIANVVTTGAFTIPL 268

Query: 248 MKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPALLYFG 307
           MKR GY+P  AGG+EA +S G QIMPP+MGA AF++AE  N P++++ K +++PA++YF 
Sbjct: 269 MKRLGYKPHQAGGIEAAASTGGQIMPPLMGAGAFLIAEYTNTPYLDVVKVSILPAIMYFA 328

Query: 308 SVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTPMFAGTIG 367
           +V+  VH+ A + G++GLPK E P     ++E W+ L+PL VLVWLL    +PM  G   
Sbjct: 329 TVYLFVHIIALKQGMQGLPKSELPQMRDVLREGWHFLLPLAVLVWLLAMHMSPMRVGFY- 387

Query: 368 LALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALVAVCW--F 425
                      A++  V+  ALR   W         FF          +A+   V W  F
Sbjct: 388 -----------AVVTMVAVAALRYTIWF--------FFVAPRQGQPVTLASTGRVIWAGF 428

Query: 426 IKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAVGENNL 485
           +K         +  L  GAR+AV V +ACA+ G+I+GVV LTG+   F+  ++A    N+
Sbjct: 429 VK--------LIEGLELGARNAVSVSLACAVAGIIVGVVGLTGLGLKFSAMMMAFSGGNI 480

Query: 486 FLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPAL-LDLGVPLIVSHMFVFYFGIMADLT 544
            L+LL+ +L  L+LGMG+P   +YI+   +  PAL  + G+PL+++H+ VF++   +++T
Sbjct: 481 VLALLMVLLASLILGMGLPVTASYIVLIVLVGPALTAEFGIPLLIAHLVVFWYSQDSNVT 540

Query: 545 PPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGG----DWGATL 600
           PP+ALA FA A IA  + +   + A + A   +++P   V+NP ++M G      W   +
Sbjct: 541 PPIALAGFAGAAIAGSKPMATGVQAWKFAKGLYLIPMFMVFNPEIIMGGPLHILAWNGLI 600

Query: 601 YMLFKAAFAVGLWGAVFTGYLQRP-MALWEKVLAFAAAASMVLAMPISDEIGFALGALFL 659
            +L   AFA  L G +FT     P +A+   ++A      MV A+ ++  I  A+GA +L
Sbjct: 601 AILALGAFAAALEGYLFTRMSWLPRIAISGAIVAVFYPNFMVEAVGVAVMI-LAIGANWL 659


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: 1353
Number of extensions: 83
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 674
Length of database: 673
Length adjustment: 39
Effective length of query: 635
Effective length of database: 634
Effective search space:   402590
Effective search space used:   402590
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