GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdcL 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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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:

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:

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:

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:

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