Alignments for a candidate for SLC13A5 in Bacillus horneckiae 1P01SC

GapMind for catabolism of small carbon sources

Alignments for a candidate for SLC13A5 in Bacillus horneckiae 1P01SC

Align Solute carrier family 13 member 5; Na(+)/citrate cotransporter; NaCT; Sodium-coupled citrate transporter; Sodium-dependent citrate transporter (characterized)
to candidate WP_066193458.1 CWS20_RS13065 SLC13 family permease

Query= SwissProt::Q8CJ44
         (572 letters)



>NCBI__GCF_002835735.1:WP_066193458.1
          Length = 549

 Score =  265 bits (676), Expect = 5e-75
 Identities = 185/556 (33%), Positives = 275/556 (49%), Gaps = 79/556 (14%)

Query: 14  FVILFFAPILLLPLIILVP----DKFARCAYVIIL-MAIYWCTDVIPVAITSLLPVLLFP 68
           FV L   P+L L  + L+P     +  R    I L ++ +W  + +P+ ITSLLP++L P
Sbjct: 62  FVGLLLGPLLFLMTVFLLPLPGLSEEGRAVLAITLWVSTWWILEAMPLGITSLLPIVLLP 121

Query: 69  LLKVLDSKQVCVQYMTDTNMLFLGSLIVATAVERWELHKRIALRMLLFVGTKPSRLMLGF 128
           L+  +   Q    Y      LFLG   +A A+E+W+LH+RIAL ++ FVGT  S L+ GF
Sbjct: 122 LMGTITGAQATASYGDPNIFLFLGGFAIALALEKWKLHERIALTIISFVGTSTSGLVYGF 181

Query: 129 MFVTAFLSMWISNTATTAMMIPIVEAMLEQMVATNVAVDASQRTMELLDKNKASELPGSQ 188
           MF T FLSMWISN AT  MMIPI  A+  ++V             EL+ K     L    
Sbjct: 182 MFATGFLSMWISNVATVMMMIPIGTAIAFKVV-------------ELMKKEGTYTL---- 224

Query: 189 VVFEDPSVQKQEDEETKNMYKAMNLCVCYAASIGGTATLTGTGPNVVLLGQMQELFPDSK 248
                        EE K   K++   + +   IGG+ATL GT PN++L G ++E++    
Sbjct: 225 -------------EEDKKFTKSIVFSIGFGGIIGGSATLIGTPPNLILAGLIKEMYGIE- 270

Query: 249 DVMNFASWFAFALPNMLLMLVMAWLWLLCFYMRPNLKKTCICCGRKKKDTEKIASKVLYE 308
             ++FA WF FA P +L++ V A      FY+      T I    K K  E     VL +
Sbjct: 271 --ISFAKWFLFAFPLILILAVFA-----AFYL------TKIAYPMKVKRLEHGRQFVL-D 316

Query: 309 EYRKLGPLSYAECNVLFCFGLLIILWFSRDPGFMPGWLSIAWIEGNTKHVTDATVAIFVA 368
           E + LG ++Y E  V   F L   +W +R         S  W +     ++D  +A+  A
Sbjct: 317 EKQALGKMTYEEKIVSIVFSLTAFMWLTR---------SFIWTD-IIPGISDTMIAMTGA 366

Query: 369 ILLFIVPSQKPKFNFSRQTEEERKTPFYPPPLLNWKVTQEKVPWGIVLLLGGGFAMAKGC 428
           ILL+++P+ K   N  R  E +               + + +PW ++LL+GGG A+A G 
Sbjct: 367 ILLYLIPASKK--NGGRILESD---------------SLKHMPWDVLLLVGGGLAIAAGF 409

Query: 429 ETSGLSEWMARQMEPLSSVRPAIITLILSCIVAMTTECTSNVATTTLFLPIFASMARSIG 488
             + LS W+  Q+  L      +I  I + +    T+   N A TT+F+PI A++A +I 
Sbjct: 410 SGTDLSTWIGSQLLLLEGTPYILILSITTILTIGITQIAPNTAITTIFVPIAATLALAID 469

Query: 489 IHPLYVMIPCTLSASLAFMLPVATPPNAIVFAYGHLKVIDMVKTGLVMNILGIASVFLSV 548
            HPL +M    L A  AFMLP+ TP  AI+F  G + ++DM++ G  + IL    +   +
Sbjct: 470 AHPLPLMAAAALGAGFAFMLPIGTPSQAIIFGTGKVTIMDMLRKGTWITILATILIITFI 529

Query: 549 NTWGRAVF--NLDKFP 562
                 VF  NL +FP
Sbjct: 530 YFLFPIVFDLNLLEFP 545


Lambda     K      H
   0.327    0.138    0.430 

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: 781
Number of extensions: 37
Number of successful extensions: 8
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: 572
Length of database: 549
Length adjustment: 36
Effective length of query: 536
Effective length of database: 513
Effective search space:   274968
Effective search space used:   274968
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: 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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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
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