GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SLC13A5 in Halomonas desiderata SP1

Align Solute carrier family 13 member 5; Na(+)/citrate cotransporter; NaCT; Sodium-coupled citrate transporter; Sodium-dependent citrate transporter (characterized)
to candidate WP_086511848.1 BZY95_RS21045 SLC13 family permease

Query= SwissProt::Q86YT5
         (568 letters)



>NCBI__GCF_002151265.1:WP_086511848.1
          Length = 532

 Score =  275 bits (702), Expect = 4e-78
 Identities = 167/500 (33%), Positives = 255/500 (51%), Gaps = 46/500 (9%)

Query: 44  LMAIYWCTEVIPLAVTSLMPVLLFPLFQILDSRQVCVQYMKDTNMLFLGGLIVAVAVERW 103
           LMA++W TE IPL+ T+L+P++L P+       Q    Y      LFLGG ++A+A+E+W
Sbjct: 64  LMAVWWMTEAIPLSATALLPIVLIPMLTERTVAQATAPYASSIVFLFLGGFLIAIAMEKW 123

Query: 104 NLHKRIALRTLLWVGAKPARLMLGFMGVTALLSMWISNTATTAMMVPIVEAILQQM-EAT 162
           NLH+RIAL TL  VG  P R++LG M  T  LSMW+SNTATT MM+PI  ++L  + E +
Sbjct: 124 NLHRRIALLTLARVGVSPHRIVLGMMLATGFLSMWVSNTATTLMMLPIGLSVLALVAERS 183

Query: 163 SAATEAGLELVDKGKAKELPGSQVIFEGPTLGQQEDQERKRLCKAMTLCICYAASIGGTA 222
             +TE      D  +A       V F         D+  KR    + L I ++AS+GG  
Sbjct: 184 GESTETVTADHDHHRA-----GHVDFIA-------DENIKRFGLCLLLAIAWSASMGGLG 231

Query: 223 TLTGTGPNVVLLGQMNELFPDSKDLVNFASWFAFAFPNMLVMLLFAWLWLQFVYMRFNFK 282
           TL G+ PN ++ G   +    +   + F  W     P     +L  W+ +  V   F  +
Sbjct: 232 TLLGSPPNAIVAGYAADELGRN---IGFLDWMLLGVPLAFTFILVGWVLMTRVLYPFKVE 288

Query: 283 KSWGCGLESKKNEKAALKVLQEEYRKLGPLSFAEINVLICFFLLVILWFSRDPGFMPGWL 342
           +  G             ++++ E RKLG L+  E  VL+ F     LW    PG +    
Sbjct: 289 EIPG-----------GQEMIEGEARKLGSLTQGEKMVLLVFGSAAFLWVV--PGVLGNIP 335

Query: 343 TVAWVEGETKYVSDATVAIFVATLLFIVPSQKPKFNFRSQTEEERKTPFYPPPLLDWKVT 402
            V    G    + D  +A+     LF++P+       R + E           +L+WK  
Sbjct: 336 GVGQWLGPLGNLDDTAIAVAAGIALFVLPA-------RGRNEM----------VLNWKDA 378

Query: 403 QEKVPWGIVLLLGGGFALAKGSEASGLSVWMGKQMEPLHAVPPAAITLILSLLVAVFTEC 462
           ++ +PWG++LL GGG +LA     +GL  W G+Q+  L  +P   +   ++ +V   TE 
Sbjct: 379 EDGLPWGVLLLFGGGLSLAGAVAGTGLDSWFGQQITGLGVLPILLLVAAVATIVLFLTEV 438

Query: 463 TSNVATTTLFLPIFASMSRSIGLNPLYIMLPCTLSASFAFMLPVATPPNAIVFTYGHLKV 522
           TSN AT   F+P+   ++  IG + + +++P   +A+ AFMLPV TPPNAIVF  G + +
Sbjct: 439 TSNTATAATFIPVLGGVAVGIGTDSMTLLIPAAFAATCAFMLPVGTPPNAIVFGTGAVSI 498

Query: 523 ADMVKTGVIMNIIGVFCVFL 542
             M + GV++NIIG+  + L
Sbjct: 499 GQMARGGVVLNIIGIVLITL 518


Lambda     K      H
   0.327    0.139    0.436 

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: 875
Number of extensions: 47
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: 568
Length of database: 532
Length adjustment: 36
Effective length of query: 532
Effective length of database: 496
Effective search space:   263872
Effective search space used:   263872
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 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