Alignments for a candidate for Dshi_1194 in Desulfoscipio geothermicus DSM 3669

GapMind for catabolism of small carbon sources

Alignments for a candidate for Dshi_1194 in Desulfoscipio geothermicus DSM 3669

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_092483139.1 BM299_RS08855 TRAP transporter permease

Query= uniprot:E4PQE4
         (729 letters)



>NCBI__GCF_900115975.1:WP_092483139.1
          Length = 727

 Score =  401 bits (1030), Expect = e-116
 Identities = 249/700 (35%), Positives = 380/700 (54%), Gaps = 59/700 (8%)

Query: 44  FVALLAIAYSAFHLYSLNIAPLETWSFRIVHIAGALVLGFVLFAGARFVSSEEGGARHRW 103
           F+ +++I  + F LY+     L +   R  H+A AL L F+L+      +++    +  W
Sbjct: 49  FIFVVSITLTLFQLYTAIFGTLISNQQRGFHVALALGLAFLLYP-----ANKRDDGKISW 103

Query: 104 TTWISAGAMLPALYVLYQTFSFWQMVQNGAMRIPVELEVWHFGWPLLAATGVGIVMSWFH 163
            + +    +L  + V+YQ          G + +PV L               G+V+  FH
Sbjct: 104 GSRVITLLLLLVVAVIYQ---------KGEISLPVALVS-------------GLVLLLFH 141

Query: 164 QRER---SVFSVP--DLVLIVCSLAVAAYFLVVYN---TSMRMSTGTSFAPVGISFAAIA 215
             +R       +P  D+VL +    V  Y    Y      + M     +   G      A
Sbjct: 142 LAKRYNQKYAGIPLFDIVLSILGFTVGLYQFFCYEGIIARVGMYNDVDYVVAG------A 195

Query: 216 GTALIMELTRRVAGMALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFSQVYTDA-GIL 274
           G  L++E  RRV G+ +V +G+  L Y + GPYLPGFL + G SV+R  S  +    G+ 
Sbjct: 196 GVLLVLEAARRVIGVPIVAVGVSMLFYAYLGPYLPGFLNHAGFSVERVISHSFLSMEGVF 255

Query: 275 GPTTAVSSTYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMIN 334
           G   ++S+T+I L+++F   LQ + +  +F + A +  G   GG AKV +  S   GMI 
Sbjct: 256 GIPISISTTFIYLYMLFGVILQRTGLEKFFSDLAMSMTGWMTGGTAKVGVLTSVFSGMIT 315

Query: 335 GTSAGNVVSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIP 394
           G+S  N V  G+ TIP+MK+ GY  + A AVEAA+STGGQIMPPIMG+ AF+M E TG+ 
Sbjct: 316 GSSVANTVGNGAFTIPMMKRAGYKPEYAAAVEAASSTGGQIMPPIMGSAAFLMIEFTGLA 375

Query: 395 YTEIAIAAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKL-RTMMKQCYLFVPIIIL 453
           Y +I  AAIIPA+L+F   +  V +E+ K  + G+  D LP +   ++K+ Y+ +PII +
Sbjct: 376 YQDIMKAAIIPALLFFTGQFIAVHYESKKLNIMGVPRDRLPSVWSLLLKKGYMLLPIIAI 435

Query: 454 IVALFMGYSVIRA-----------GTLATVSAAVVSW--LSPNKMGLRHILQALEIASYM 500
           +V L  G S ++A             LA + A ++    +  +K+ L    Q L  A+  
Sbjct: 436 VVILCTGQSAMKAALYGIYTSLGMSVLALIIAKILGKQDMIEDKLTLPVFFQILADAART 495

Query: 501 AIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAATSQLLALIFAMFISILLGMGMPTT 560
           A+ +I  CAAAGVI GVI+LTG+G + S  +L +A    +L + F M  SI+LGMG+PTT
Sbjct: 496 ALPVIAACAAAGVIAGVITLTGLGLKISGGILSLAHNKLILTMFFTMIASIILGMGLPTT 555

Query: 561 AAYAVAASVVAPGLVQLGIEP-LTAHFFVFYFAVVSAITPPVALASYAAAGISGANAMET 619
           A Y + A++ AP L+     P + AH FVFYF +V+ ITPPVALA+YA AG++ +N  +T
Sbjct: 556 ANYVITATMAAPALLAFDSVPVIAAHMFVFYFGIVADITPPVALAAYAGAGLANSNPFQT 615

Query: 620 SVASFRIGIAAFIVPFMFFYNGALLME-AGWFEIARALVTATFGVYMLSGGVLGWFASIS 678
            V + +I I AF++P+MF  +  LLME A  F++   +V A  G++ +S  + G F    
Sbjct: 616 GVQAVKIAIGAFLIPYMFVLSPVLLMENATLFKLVIVIVAAMLGMFCISVSLAG-FMEKK 674

Query: 679 ASWITRLLLIAAALLMIEGGLWTDLTGIALAVLAFVIQKQ 718
            S I R+LLI A L ++   L +DL G+ +    F+ QK+
Sbjct: 675 LSIIERVLLIPAGLALVNPWLLSDLFGLVILAAVFLYQKR 714


Lambda     K      H
   0.327    0.139    0.410 

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: 1237
Number of extensions: 75
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: 729
Length of database: 727
Length adjustment: 40
Effective length of query: 689
Effective length of database: 687
Effective search space:   473343
Effective search space used:   473343
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 Apr 09 2024. 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 2024 update 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