Alignments for a candidate for SLC13A5 in Halopiger salifodinae KCY07-B2

GapMind for catabolism of small carbon sources

Alignments for a candidate for SLC13A5 in Halopiger salifodinae KCY07-B2

Align Solute carrier family 13 member 2 (Na /di- and tricarboxylate cotransporter 1) (NaDC-1) (Renal sodium/dicarboxylate cotransporter) (characterized)
to candidate WP_049988637.1 LT39_RS01170 anion transporter

Query= TCDB::Q13183
         (592 letters)



>NCBI__GCF_000784335.1:WP_049988637.1
          Length = 541

 Score =  212 bits (540), Expect = 3e-59
 Identities = 167/552 (30%), Positives = 254/552 (46%), Gaps = 63/552 (11%)

Query: 16  IVFFVPILLLPLPILVPSKEAYCAYAIILMALFWCTEALPLAVTALFPLILFPMMGIVDA 75
           ++  V I   P P  +     Y    +    + W T A PLAVTAL   +L    GI D 
Sbjct: 20  VIGTVAIAAAPTPSGLEISGQYAIATMFFAGVLWVTGAFPLAVTALTIPVLLTGTGIYDD 79

Query: 76  SEVAVEYLKDSNL-LFFGGLLVAIAVEHWNLHKRIALRVLLIVGVRPAPLILGFMLVTAF 134
            + A+    D  + LF  G ++A A++ +N+ +RIAL  ++ +G  P  LIL  MLVTA 
Sbjct: 80  MDTALAGFADHLIFLFLAGFMLANAIQKYNIDRRIALYSMVKMGSSPRRLILAVMLVTAG 139

Query: 135 LSMWISNTATSAMMVPIAHAVLDQLHSSQASSNVEEGSNNPTFELQEPSPQKEVTKLDNG 194
           LSMW+SNTAT+AMM PIA  VL Q+ S    ++ ++ +                   +  
Sbjct: 140 LSMWVSNTATTAMMTPIAVGVLTQVLSRDELASADQAA-------------------ETT 180

Query: 195 QALPVTSASSEGRAHLSQKHLHLTQCMSLCVCYSASIGGIATLTGTAPNLVLQGQINSLF 254
            A    +AS  G A ++ +  +L   M L   Y+ASIGG+ T+ GT PN +L GQ+N++ 
Sbjct: 181 DAAGTAAASDGGTAEVAPEFTNLQIGMLLGTAYAASIGGVGTIIGTPPNAILVGQLNAVL 240

Query: 255 PQNGNVVNFASWFSFAFPTMVILLLLAWLWLQILFLGFNFRKNFGIGEKMQEQQQAAYCV 314
                 + FA W    FP +V+ L L W+ L  +               + + + AA   
Sbjct: 241 DYE---IGFADWLLIGFPVVVVTLPLVWVLLTYVLYPPEI-------TGVDDARAAAREQ 290

Query: 315 IQTEHRLLGPMTFAEKAISILFVILVLLWFTREPGFFLG------WGNLAFPNAKGESMV 368
           +  E    G ++   K ++++F     LW     G F        W    F    G+   
Sbjct: 291 LAEE----GALSPRGKRVAMIFAATAGLWVLGGLGEFFDPYLPSVWMTTLF---GGDGAT 343

Query: 369 SDGTVAIFIGIIMFIIPSKFPGLTQDPENPGKLKAPLGLLDWKTVNQKMPWNIVLLLGGG 428
             G VA   G++ +++     G+   P            ++W  +   + W  +LL GGG
Sbjct: 344 VFG-VAGHQGLLYYVM----VGVAAVP-----ALVLADTMEWDEL-VDIDWGTLLLFGGG 392

Query: 429 YALAKGSERSGLSEWLGNKL-TPLQSVPAPAIAIILSLLVATFTECTSNVATTTIFLPIL 487
            +LA     +G +EW+   + + L   P   +   + LLV   TE TSN ATT+I +PIL
Sbjct: 393 ISLANALADTGATEWIAETVFSGLVGAPILLVIAAVVLLVVFLTEMTSNAATTSIIVPIL 452

Query: 488 ASMAQAICL--------HPLYVMLPCTLATSLAFMLPVATPPNAIVFSFGDLKVLDMARA 539
            S+                L++ +  T+A S AF LPVATPPNAIVF  G ++   M R 
Sbjct: 453 ISLGSVFSATLGLSDFSTALFLAVAGTIAASFAFALPVATPPNAIVFGSGYVEQRHMLRT 512

Query: 540 GFLLNIIGVLII 551
           G +LN I   ++
Sbjct: 513 GLILNAIMTAVL 524


Lambda     K      H
   0.325    0.138    0.429 

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: 749
Number of extensions: 38
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 592
Length of database: 541
Length adjustment: 36
Effective length of query: 556
Effective length of database: 505
Effective search space:   280780
Effective search space used:   280780
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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
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