GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SLC13A5 in Nocardiopsis lucentensis DSM 44048

Align tonoplast dicarboxylate transporter (characterized)
to candidate WP_017600457.1 D471_RS0121060 DASS family sodium-coupled anion symporter

Query= CharProtDB::CH_091173
         (540 letters)



>NCBI__GCF_000341125.1:WP_017600457.1
          Length = 533

 Score =  274 bits (700), Expect = 7e-78
 Identities = 178/546 (32%), Positives = 276/546 (50%), Gaps = 40/546 (7%)

Query: 5   DVTVAGSDDLKSPLLPVVHNDEPFERQTVGQQLRTIFTPKNCYIALGPLLCAVVC-LCVD 63
           D  V   D    P  PV     P ++        T   P+   + LGP+L  +V  L  D
Sbjct: 5   DPAVNAPDSASVPRQPV-----PQDKDRASGNRETNPLPRRIGLVLGPVLGLLVYFLLPD 59

Query: 64  LG---------GDETTTARNMLGVLVWMFAWWLTEAVPMPITSMTPLFLFPLF--GISAA 112
           +          GD     R + G+ V++  WW TEA+P+P+TS+ PL  FP+   G+ A 
Sbjct: 60  MPLPLPDGEGMGDLAVNGRAVAGITVFIATWWATEAIPIPVTSLVPLVAFPILVDGV-AV 118

Query: 113 DDVANSYMDDVISLVLGSFILALAVEHYNIHRRLALNITLVFCVEPLNAPLLLLGICATT 172
            DVA SY    I L +G F+LALA++ +N+H+R+AL  T+V  V   N   L+ G    T
Sbjct: 119 GDVAPSYGSPTIFLFMGGFMLALAMQRWNLHKRIAL--TIVSKVGS-NTVGLIGGFMVAT 175

Query: 173 AFVSMWMHNVAAAVMMMPVATGILQRLPS-SSSTTEVVHPAVGKFSRAVVLGVIYSAAVG 231
           AF+SMW+ N A  VMM+PV   ++  +       T+        F+ A++LG+ Y+A++G
Sbjct: 176 AFISMWVSNTATTVMMLPVGLSVVALITQFRGGRTDA------NFATALMLGIAYAASIG 229

Query: 232 GMSTLTGTGVNLILVGMWKSYFPEADPISFSQWFFFGFPLALCIFVVLWCVLCVMYCPKG 291
            ++TL GT  N+++V     +      I F QW   G P+A+    + W VL  +    G
Sbjct: 230 SVATLIGTPPNVLMVAYLSEFHDIT--IGFGQWMMVGLPIAVAFLFLAWVVLARLLFRPG 287

Query: 292 AGQALSPYLHKSHLRRELDLLGPMNFAEKMVLAVFGGLVVLWMTRNITDDIP--GWGRIF 349
             +       +  +R EL  +GP++  EK+VLAVF    + W+   +  D    G    +
Sbjct: 288 VKRVEGA---QELIRDELREMGPISRPEKLVLAVFVTAALSWIFVPMRADSQTIGGALPW 344

Query: 350 AGRAGDGTVSVMMATLLFIIPSNIKKGEKLMDWNKCKKLPWNIVLLLGAGFAIADGVRTS 409
            G   D  +++ +A  LF+IP+    G +L+DW+   KLPW I+LL G G AI+     S
Sbjct: 345 LGGISDPVIAMAVAVALFLIPAERGTGTRLLDWDTAVKLPWGILLLFGGGIAISGQFTAS 404

Query: 410 GLAEVLSKGLVFLETAPYWAIAPTVCLIAATITEFTSNNATTTLLVPLLIEIAKNMGIHP 469
           GL+  +   +  L   P W +   V  +   +TE TSN ATT+  +P+L  +A  + +  
Sbjct: 405 GLSVWIGGQVSVLGGVPIWVLVLCVTAVVLLLTELTSNTATTSTFLPVLGGVAAGLDVDV 464

Query: 470 LLLMVPGAIGAQFAFLLPTGTPSNVVGFTTGHIEIKDMIKTGLPLKIAGTIFLSILMPTL 529
           L+L+VP  + A  AF+LP  TP N + F +GHI I  M++ G+ L +A     ++ +  L
Sbjct: 465 LVLVVPAVLAASMAFMLPVATPPNAIVFGSGHITINQMMRGGVLLNLA-----ALFVVLL 519

Query: 530 GAYVFA 535
           G Y  A
Sbjct: 520 GMYALA 525


Lambda     K      H
   0.326    0.140    0.441 

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: 928
Number of extensions: 52
Number of successful extensions: 7
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: 540
Length of database: 533
Length adjustment: 35
Effective length of query: 505
Effective length of database: 498
Effective search space:   251490
Effective search space used:   251490
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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