Alignments for a candidate for Psest_0084 in Archaeoglobus veneficus SNP6

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Archaeoglobus veneficus SNP6

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_013683146.1 ARCVE_RS02185 C4-dicarboxylate ABC transporter

Query= uniprot:E4PQE4
         (729 letters)



>NCBI__GCF_000194625.1:WP_013683146.1
          Length = 673

 Score =  372 bits (954), Expect = e-107
 Identities = 211/580 (36%), Positives = 330/580 (56%), Gaps = 47/580 (8%)

Query: 172 VPDLVLIVCSLAVAAYFLVVYNTSM-RMSTGTSFAPVGISFAAIAGTALIMELTRRVAGM 230
           V DL+L +    VA Y  + Y+  + R + G +     IS     G  L++E TRR    
Sbjct: 83  VYDLILAIIGAYVALYITINYSDLIHRAAIGYNTMDYVIS---AMGIILVLEATRRAVNP 139

Query: 231 ALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFSQVY-TDAGILGPTTAVSSTYIILFI 289
           A+ +I +VF+ Y   G  LPG L +P  + +     +Y T  G+ G   AVS+T+++LFI
Sbjct: 140 AMAVIVIVFILYAKYGANLPGVLSHPPYTWKEVLEHLYLTKEGVFGTPLAVSATFVVLFI 199

Query: 290 IFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTI 349
           IF AFL+ S  G +F++ A++  G   GGPAK ++ AS LMG ++G+S  N V+TG+ TI
Sbjct: 200 IFGAFLEKSGAGKFFIDLAYSITGGMVGGPAKAAVMASALMGTVSGSSVANTVTTGTFTI 259

Query: 350 PLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILY 409
           PLMK+VGY  + AGAVE AASTGGQI+PP+MGA AFIMAE  G+PY  IA AA+IPA+LY
Sbjct: 260 PLMKRVGYKPEFAGAVEPAASTGGQILPPVMGAAAFIMAEFVGMPYVTIAYAALIPALLY 319

Query: 410 FASVYFMVDFEAAKTGMRGMREDELPKLRTMMK-QCYLFVPIIILIVALFMGYSVIRAGT 468
           F  V+  VD EA K  +RG+  +ELP+   ++K   Y  VP+ +L+  L  G++ I A  
Sbjct: 320 FFGVFTAVDLEARKENLRGLPREELPRTLDVLKGGWYYLVPLFVLVHMLVHGFTPILAAI 379

Query: 469 LATVSAAVVSWLSP------------------NKMGLRHILQALEIASYMAIQIIVVCAA 510
            A +S   +  + P                   K  L + ++AL      A+ + + CA+
Sbjct: 380 YAILSVVAIMIIKPIYENLKRPKGERLPAGVLAKNILSNFIEALNSGGRGAVAVAIACAS 439

Query: 511 AGVIVGVISLTGVGARFSVLLLDVAATSQLLALIFAMFISILLGMGMPTTAAYAVAASVV 570
           AG+IVGV++LTG+G + +   + ++    L  L+  MF+S++LGMG+PTTA Y + +++ 
Sbjct: 440 AGIIVGVVTLTGLGFKIAAEAVTISNGQLLPILLLTMFVSLMLGMGVPTTANYIITSTIA 499

Query: 571 APGLVQ-------------LGIEP---LTAHFFVFYFAVVSAITPPVALASYAAAGISGA 614
           AP ++              L   P   L AH FVFYF V + +TPPVALA+YA + I+G+
Sbjct: 500 APAIITFMAANAGMNVRDFLAAYPELVLPAHMFVFYFGVAADLTPPVALAAYAGSAIAGS 559

Query: 615 NAMETSVASFRIGIAAFIVPFMFFYNGALLMEAGWFEIARAL------VTATFGVYMLSG 668
           +  +T + + +IGI  ++VP++F Y+  +L+    F +   +      +    G+  ++G
Sbjct: 560 DPWKTGINAAKIGIGKYLVPYVFIYSPIILLLNLSFSLPDIINLLWIVLCVMLGIVAING 619

Query: 669 GVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIAL 708
             +G+      S  TR+ L+   +L++   L++ + G+ L
Sbjct: 620 ATIGYLLR-PCSKATRMFLLIPGILLLAPSLYSKIAGLIL 658


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: 1152
Number of extensions: 54
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: 729
Length of database: 673
Length adjustment: 39
Effective length of query: 690
Effective length of database: 634
Effective search space:   437460
Effective search space used:   437460
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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