Alignments for a candidate for Dshi_1194 in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for Dshi_1194 in Halomonas desiderata SP1

Align TRAP transporter (characterized, see rationale)
to candidate WP_086511837.1 BZY95_RS20990 C4-dicarboxylate ABC transporter permease

Query= uniprot:A8LI82
         (743 letters)



>NCBI__GCF_002151265.1:WP_086511837.1
          Length = 720

 Score =  796 bits (2055), Expect = 0.0
 Identities = 431/730 (59%), Positives = 523/730 (71%), Gaps = 27/730 (3%)

Query: 4   QTKTADDHLIAEGVDEEPTESNRRLFEGRNFILISTFAALYAAFHMAALNGLSISEWTGI 63
           Q + A   +  EGV + P   N R+  G     +     L+ A H+ ALN          
Sbjct: 6   QPEQAASKIGTEGVADIPIAHNERVLSGLLGQTVFAACVLFTAMHLYALN---------- 55

Query: 64  EVPFLPTFPMETWNFRIVHIAGALALGFLLFAARTDFPGPGKETPLLGYVAYGLMVPALF 123
                   P+ETW FRI+H+AG LA+GF + AA T    PG+    +G V +  M+PA+ 
Sbjct: 56  ------VSPIETWAFRIIHVAGGLAVGFAITAAYTLDRSPGERH--IGKVEWLAMIPAVA 107

Query: 124 SLGMAASFSMEIASGVMWNGIDEGIKFNETWLF---GLPLIVATAGGIVLSWFHKRARSG 180
           ++  AA      A G  W   +        W+       L +AT   ++ SW  + +   
Sbjct: 108 AIVYAA-----FAIGYAWFIRETQGTPPAGWVLVHMSWALTIATGIAMISSWIWRGSSRS 162

Query: 181 FSAPDLVLAICGVAVATYLITIYGTLMRNSTGTPFAPIGISIAAVAGTALIMELTRRVAG 240
               D VL +  + VA YL+ +     R + GTPFA     + +  G ALIMELTRRVAG
Sbjct: 163 VHWADAVLIVASIIVAAYLLFVLQR-WRMAAGTPFAGQTEFLVSAIGVALIMELTRRVAG 221

Query: 241 MALIVIAGIFLAYVFVGQYLPGFLNAPAVTWQRFFSQVYTDAGILGPTTAVSSTYIILFI 300
           +ALIVI  +FL Y F G YLPG L     + QRFF+ +YTD GILG TTAVSSTYIILFI
Sbjct: 222 LALIVITAVFLVYAFAGPYLPGLLEHRGYSPQRFFTYLYTDNGILGATTAVSSTYIILFI 281

Query: 301 IFAAFLQASKVGDYFVNFAFAAAGQSRGGPAKVAIFASGLMGMINGTSAGNVVATGSLTI 360
            FAAFLQAS+VGDYFVNFAFAAAG++RGGPAKVA+FASGLMGMINGTSAGNVVATGSLTI
Sbjct: 282 TFAAFLQASRVGDYFVNFAFAAAGRARGGPAKVAVFASGLMGMINGTSAGNVVATGSLTI 341

Query: 361 PLMKKVGYHKKTAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIALAAIIPAILY 420
           PLMKKVGYH ++AG +EAAASTGGQI+PPIMGAGAFIMAEITGIPYTEIA+AA+IPA LY
Sbjct: 342 PLMKKVGYHPRSAGGIEAAASTGGQIVPPIMGAGAFIMAEITGIPYTEIAIAALIPAALY 401

Query: 421 FVSVYFMVDLEAAKLGMRGMSRDELPKFNKMVRQVYLFLPIIILIYALFMGYSVIRAGTL 480
           F+S+Y MVDLEA + GM+G+ +D+LP F  MV+QVYLFLPIIILI  LFMGYSVIRAGTL
Sbjct: 402 FLSIYLMVDLEARRGGMQGLPKDQLPVFRSMVKQVYLFLPIIILIGTLFMGYSVIRAGTL 461

Query: 481 ATVAAAVVSWFTPFRMGPRSIAKAFEIAGTMSVQIIAVCACAGIIVGVISLTGVGARFSA 540
           A V+AAVVSWFTP  MGP+++  A  +   M++ +IAVCACAGIIVGVI+LTGVGARF++
Sbjct: 462 AMVSAAVVSWFTPHWMGPKALLNALSLGARMAIPLIAVCACAGIIVGVIALTGVGARFAS 521

Query: 541 VLLGIADTSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAPGLVQLGIPLLTAHFFVF 600
           +LLGIAD S LLALFFAMCI+ILLGMGMPTTAAYAVAASVVAPGL Q+GIP L AHFFVF
Sbjct: 522 MLLGIADASHLLALFFAMCISILLGMGMPTTAAYAVAASVVAPGLQQIGIPPLVAHFFVF 581

Query: 601 YFAVLSAITPPVALASYAAAGISGANPMETSVTSFKIGIAAFIVPFMFFYNSAILMDGTW 660
           Y+AVLSAITPPVALA YAAA ISG +P++T++TSFK G+AAFIVPFMFFY+ A+LMDGTW
Sbjct: 582 YYAVLSAITPPVALAGYAAAAISGTDPLKTAMTSFKFGLAAFIVPFMFFYSPALLMDGTW 641

Query: 661 FEVLRAGATAVVGVFFLSSGVQGWFMGGRAAWFLRVGLVFAALMLIEGGIMSDLIGVGTA 720
            ++LR   TA VG++ L++ VQGWF+ G      RV L+ AAL +I GG M+DL+GVG  
Sbjct: 642 MQILRVALTAGVGIYLLAASVQGWFLNGGVNLVQRVLLLAAALSMIAGGWMTDLLGVGIG 701

Query: 721 VAIFLIQKLA 730
             +F+ Q  A
Sbjct: 702 GLVFVWQAAA 711


Lambda     K      H
   0.327    0.140    0.419 

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: 1657
Number of extensions: 85
Number of successful extensions: 4
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: 743
Length of database: 720
Length adjustment: 40
Effective length of query: 703
Effective length of database: 680
Effective search space:   478040
Effective search space used:   478040
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 (21.7 bits)
S2: 55 (25.8 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