Alignments for a candidate for sdc in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdc in Echinicola vietnamensis KMM 6221, DSM 17526

Align The Na+-coupled dicarboxylate (succinate; malate; fumarate) transporter, SdcL (transports aspartate, α-ketoglutarate and oxaloacetate with low affinity). Km for succinate, ~6 (characterized)
to candidate Echvi_3555 Echvi_3555 anion transporter

Query= TCDB::Q65NC0
         (546 letters)



>FitnessBrowser__Cola:Echvi_3555
          Length = 485

 Score =  509 bits (1312), Expect = e-149
 Identities = 252/485 (51%), Positives = 338/485 (69%), Gaps = 8/485 (1%)

Query: 57  QKIGLLLGPALFFAVLLFFFPEGLSYEGRMVLATTLWVAVWWITEAVPIPAASLLPIVLL 116
           ++ GL+LGP  F  ++LFF P+GL+YE + VLA  +W+A+WWI EA+PI A +LLP+V+L
Sbjct: 7   KRSGLVLGPVAFLLIVLFFNPDGLTYEAQAVLALAVWMAIWWILEAIPIAATALLPLVIL 66

Query: 117 PLTGALEGAAVTSSYGDPIVFLFLGGFLIALAMERWNLHKRIALNIISVVGTSTSRIVLG 176
           PLTGAL      + Y DP V L++GGF+IA+ +E+WNLHKRIAL+IIS++GT    IVLG
Sbjct: 67  PLTGALSMDESAAPYADPKVLLYMGGFMIAVTIEKWNLHKRIALSIISLIGTDMRFIVLG 126

Query: 177 FMAATGFLSMWVSNTAAVMMMLPIGTAIIHQVSAVIKSERKDLAAEEAKFSKALIFSIGY 236
           FM AT  LSMW+SNTA  +MMLPI  A+IHQ++        +++A   +  +AL+  I Y
Sbjct: 127 FMLATALLSMWISNTATSLMMLPIAVAVIHQLA----DGSDEISA--TRIGQALMLGIAY 180

Query: 237 AGTIGGLGTLIGTPPNIILAANIKKLYGVEVSFGGWMAFAVPVVVILLVAVWLYLTKVAH 296
           + +IGGL T+IGTP NI+L   +K+LYG+E+ F  WM   +P+ + LL   W YL  VA+
Sbjct: 181 SASIGGLATIIGTPTNIVLVGIVKELYGIEIGFAEWMLVGLPISLGLLGICWWYLVSVAY 240

Query: 297 PI-KMKELPGGKELILEEKRKLGKMSFEETMVLLVFGFAAFMWVTRTFLWDDKIPGIDDT 355
           P  K   L GGK  I  +   +G +S  E  VLLVF   +F W+TR FL  D +P ++DT
Sbjct: 241 PFPKNMSLAGGKVEIQRQLAAIGPISKPEIRVLLVFLLVSFSWITRVFL-QDLLPFLNDT 299

Query: 356 MIAIFAASLLFLIPSLNKGGRVLDWSVSKDLPWGILLLFGGGLALATGFKETGLAEWIGG 415
           +IA+    LLF++PS     R+LDW  ++D+PWGILLLFGGGLALA GFKETGLA W+G 
Sbjct: 300 IIALVGVLLLFMLPSSRGKKRLLDWKTAEDIPWGILLLFGGGLALAAGFKETGLAAWLGS 359

Query: 416 RLTVLDGFNFVVIVIISTALVLFLTEITSNTATATMILPVLASLALALNVHPYALMVPAA 475
               L G +F++ ++I  A V FLTEITSN ATA+M+LP+L ++ALAL VHPY LMV A 
Sbjct: 360 HFEALQGVHFLLFILIIVASVNFLTEITSNVATASMLLPILGAVALALGVHPYGLMVAAT 419

Query: 476 MAANCAFMLPVGTPPNAIIFASGKLKISEMVRTGFVINIFTLILIVGAVFYILPHLWGVD 535
           MAA+CAFMLPV TPPNA++F SG L I  M + G  +NI ++  I   V+YI+P LWG+D
Sbjct: 420 MAASCAFMLPVATPPNAVVFGSGYLTIPAMAKAGLWMNILSIFFITLFVYYIMPFLWGID 479

Query: 536 LTVFP 540
           L V+P
Sbjct: 480 LKVYP 484


Lambda     K      H
   0.326    0.140    0.425 

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: 811
Number of extensions: 42
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: 546
Length of database: 485
Length adjustment: 35
Effective length of query: 511
Effective length of database: 450
Effective search space:   229950
Effective search space used:   229950
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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

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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, or view the source code.

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