Alignments for a candidate for SLC26dg in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for SLC26dg in Marinobacter adhaerens HP15

Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate GFF1051 HP15_1030 sulfate permease family protein

Query= TCDB::Q1J2S8
         (499 letters)



>FitnessBrowser__Marino:GFF1051
          Length = 495

 Score =  602 bits (1551), Expect = e-176
 Identities = 313/487 (64%), Positives = 377/487 (77%), Gaps = 4/487 (0%)

Query: 17  WFANPRKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISA 76
           W +N R DVLAGIVVALALIPEAIAFSIIAGVDP+VGLYASF IA+I AF+GGRPGMISA
Sbjct: 9   WLSNIRGDVLAGIVVALALIPEAIAFSIIAGVDPKVGLYASFCIAVIIAFVGGRPGMISA 68

Query: 77  ATGAMALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALA 136
           AT AMA+LM  LVK+HG+QYL AAT++TGVLQ++ G+ KL   ++FV RSV+ GFVNALA
Sbjct: 69  ATAAMAVLMVTLVKEHGLQYLLAATLMTGVLQLIAGYLKLGSLMRFVSRSVVTGFVNALA 128

Query: 137 ILIFMAQLPQFVGANWQMYAMVAAGLAIIYL---LPLVFKAMPSALVAIVVLTVVAVVTG 193
           ILIFMAQLP+     W +YAM AAGL IIYL   LP+V K +PS LV IVVLT VAVVTG
Sbjct: 129 ILIFMAQLPELTNVTWHVYAMTAAGLGIIYLFPLLPVVGKVLPSPLVCIVVLTAVAVVTG 188

Query: 194 ADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQLIDERT 253
            D++TVGDMG LP  LP F +P VPL  ETL II P ++ L++VGLLES++TA ++D+ T
Sbjct: 189 MDIRTVGDMGDLPDTLPVFLWPDVPLNLETLMIILPYSIPLAIVGLLESMMTATIVDDLT 248

Query: 254 DTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGAFLMVLI 313
           DTTSD+N E +GQG+ANI +G  GGMAGCAMIGQS+INV SGGR RLST  AG FL+V++
Sbjct: 249 DTTSDRNRECKGQGIANIGSGLIGGMAGCAMIGQSIINVKSGGRTRLSTLTAGLFLLVMV 308

Query: 314 LALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVTVFTHDLS 373
           L L  +LVQIPMAALVAVM++V+I TF W S+R L   P    +VML TV V V TH+L+
Sbjct: 309 LLLDSVLVQIPMAALVAVMIMVSIGTFSWDSIRNLREHPLSTNIVMLVTVIVVVATHNLA 368

Query: 374 LGVLIGVVLSALFFARKVSQLSQVT-PVDEVDGTRTYRVRGQLFFVSTHDFLHQFDFTHP 432
            GVL GV+L+ALFFA KV     VT  +DE   TRTYRV GQ+FF S+  F+  FDF   
Sbjct: 369 FGVLAGVLLAALFFANKVGHYMLVTSELDETTDTRTYRVVGQVFFSSSEKFMESFDFKEA 428

Query: 433 ARRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLNAASATLVERLAVHDKPDA 492
              VVIDLS AHFWD +AVGALDK ++KF R+G+ VE+ GLN ASAT+V+R  VHDKPDA
Sbjct: 429 VDNVVIDLSRAHFWDITAVGALDKAVIKFRREGSEVEVIGLNEASATIVDRFGVHDKPDA 488

Query: 493 LDRMGGH 499
           +D++ GH
Sbjct: 489 VDQLMGH 495


Lambda     K      H
   0.328    0.140    0.407 

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: 572
Number of extensions: 26
Number of successful extensions: 3
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: 499
Length of database: 495
Length adjustment: 34
Effective length of query: 465
Effective length of database: 461
Effective search space:   214365
Effective search space used:   214365
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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