Alignments for a candidate for Psest_0084 in Desulfacinum hydrothermale DSM 13146

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Desulfacinum hydrothermale DSM 13146

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_084056391.1 B9A12_RS03675 permease

Query= uniprot:E4PQE4
         (729 letters)



>NCBI__GCF_900176285.1:WP_084056391.1
          Length = 630

 Score =  388 bits (997), Expect = e-112
 Identities = 211/554 (38%), Positives = 333/554 (60%), Gaps = 10/554 (1%)

Query: 174 DLVLIVCSLAVAAYFLVVYNTSMRMSTGTSFAPVGISFAAIAGTALIMELTRRVAGMALV 233
           DLVL+  SLAVA Y ++  +         S   V +    I    L++E TRRV G  ++
Sbjct: 80  DLVLVAASLAVAGYIVLDLDGIFARQGDWSSWDVTVGILCIL---LVLEATRRVIGPMMM 136

Query: 234 IIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFSQV-YTDAGILGPTTAVSSTYIILFIIFA 292
            IG++FL Y + GPY+P  + + G SV+R  + +  T  G+ G    V++T++ +FI+F 
Sbjct: 137 AIGVIFLLYGYFGPYMPDLIIHRGYSVERIATTLSLTTEGVFGLPIGVAATFVFIFILFG 196

Query: 293 AFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTIPLM 352
           AFL  +  G++F++ A++  G+  GGPAK ++ ASG MG ++G++  NVVSTGS TIP+M
Sbjct: 197 AFLDKTGGGNFFIDLAYSLTGQFSGGPAKTAVLASGFMGSVSGSAVANVVSTGSFTIPMM 256

Query: 353 KKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILYFAS 412
           K+VGY    AGA+EAAASTGGQ+MPPIMGAGAF+MAE T  PY  I   A+IPA+LY+ +
Sbjct: 257 KRVGYRPHVAGAIEAAASTGGQLMPPIMGAGAFLMAEFTNTPYLHIIKVALIPAVLYYMT 316

Query: 413 VYFMVDFEAAKTGMRGMREDELPKL-RTMMKQCYLFVPIIILIVALFMGYSVIRAGTLAT 471
               V  EA K G+ G  +++LPK+  T+ K  +  +P+ ILI  L M +S + AG +A 
Sbjct: 317 TLLFVHIEAKKEGLEGQPKEDLPKMGETLKKGVHFLIPLAILITVLLMNFSPMMAGFIAV 376

Query: 472 VSAAVVSWL-SPNKMGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVL 530
           VS    + L   +++ L  ++ ALE  +  A+ + + CAAAG+IVG+ +LTG+G RFS +
Sbjct: 377 VSVYATAMLRKQSRLSLSKLISALETGARNAVMVSIACAAAGIIVGITNLTGMGLRFSSM 436

Query: 531 LLDVAATSQLLALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFY 590
           ++ ++    LLA+      S+ LGMG+P TA+Y V   +  P L+ +GI  +TAH  VF+
Sbjct: 437 VVSLSHGIPLLAIGLIALASLALGMGLPVTASYIVLVILAGPALMDMGIPLITAHMIVFW 496

Query: 591 FAVVSAITPPVALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEAGWF 650
           ++  + +TPPV+LAS+A AGI+G++ M T+  S+++    +I+P +  Y+  LL+     
Sbjct: 497 YSQDANVTPPVSLASFAGAGIAGSSPMRTAFTSWKLAKGLYIIPVVMAYH-PLLLNGPAG 555

Query: 651 EIARALVTATFGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIALAV 710
           E+ R +V     +      +  +F +    W+   L  A+A+ MI  G   +  G+ L  
Sbjct: 556 EVVRTIVGTALALLAFVVAMERYFLA-PIGWVETALYAASAVAMIWVGRGINYAGMGLFA 614

Query: 711 L--AFVIQKQRKTR 722
           L  A+ ++  R+ +
Sbjct: 615 LLVAYHVKTARRAK 628



 Score = 32.7 bits (73), Expect = 6e-05
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 33 NRRL--FEGGLLKFVALLAIAYSAFHLYSLNIAPLETWSFRIVHIAGALVLGFV 84
          NR L  F G + K V ++A++ S F LY+  +  +     R VH+   LVL F+
Sbjct: 7  NRSLSGFPGTIAKVVTVVAVSLSLFQLYTAGLGAMTAMVQRSVHLGLILVLTFL 60


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: 1162
Number of extensions: 76
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 729
Length of database: 630
Length adjustment: 39
Effective length of query: 690
Effective length of database: 591
Effective search space:   407790
Effective search space used:   407790
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: 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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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