GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galP in Halococcus hamelinensis 100A6

Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate WP_007692967.1 C447_RS08630 sugar porter family MFS transporter

Query= SwissProt::P0AEP1
         (464 letters)



>NCBI__GCF_000336675.1:WP_007692967.1
          Length = 470

 Score =  310 bits (795), Expect = 5e-89
 Identities = 174/447 (38%), Positives = 262/447 (58%), Gaps = 6/447 (1%)

Query: 9   RSNKAMTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSSMMFGAAVG 68
           R +    + + F+ AL GLLFG D GVIAGALP+I + F +++  QE V  S++ GA +G
Sbjct: 12  REHPRFVYVMAFVGALNGLLFGFDTGVIAGALPYIQETFTLSTFLQEVVTVSVLVGAMIG 71

Query: 69  AVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPL 128
           A   G L+ + GR++  ++GA++F   +L  A +P+VE LI  R++LG+AVG+AS   PL
Sbjct: 72  AATGGRLADRFGRRRLTLVGAVIFFVAALGLAVSPSVEWLIGWRIVLGVAVGIASLIGPL 131

Query: 129 YLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAF--SYTG--AWRWMLGVIIIPAILL 184
           Y+SE APE IRG++  + QLMI +GIL AY+ +  F  S  G   WRWMLG   +PA++L
Sbjct: 132 YISETAPEDIRGTLGFLQQLMIVVGILVAYVVNAIFAPSLLGIIGWRWMLGFAAVPAVIL 191

Query: 185 LIGVFFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQVKQSGWALFKE 244
            + +FFLP+SPRW     R  +A  VL R+R+  A+ + E+  + E  + +  G      
Sbjct: 192 GVTMFFLPESPRWLVEHDRHDEARDVLSRIRN-EADFESEIQRMEEISERESEGSWRDVL 250

Query: 245 NSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLTNVLAT 304
               R A+ +GV L V+QQ TG+N ++YYAP I +  G   +   ++GT+ +G+ NV  T
Sbjct: 251 EPWIRPALTVGVALAVLQQVTGINTVLYYAPTILQNIG-LGSAASLFGTIGIGIVNVALT 309

Query: 305 FIAIGLVDRWGRKPTLTLGFLVMAAGMGVLGTMMHIGIHSPSAQYFAIAMLLMFIVGFAM 364
            +A+   DR GR+P L +    M   +G LG   ++   S    YF +  +++++  FA+
Sbjct: 310 IVAVYYADRIGRRPLLLVSVGGMTVMLGALGLGFYLPGLSGVVGYFTLGSMILYVAFFAL 369

Query: 365 SAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFWVYAAL 424
             GP+ W+L SEI PL+ R      +T  NW AN+IV  TFL+++   G   +FW     
Sbjct: 370 GLGPVFWLLTSEIFPLRVRGTAEGITTFFNWSANLIVSLTFLSLIERFGQTASFWALGFF 429

Query: 425 NVLFILLTLWLVPETKHVSLEHIERNL 451
            VL  +   + VPET   SLE IE +L
Sbjct: 430 GVLGFVYIYFRVPETMGRSLEDIEDDL 456


Lambda     K      H
   0.327    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: 827
Number of extensions: 56
Number of successful extensions: 5
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: 464
Length of database: 470
Length adjustment: 33
Effective length of query: 431
Effective length of database: 437
Effective search space:   188347
Effective search space used:   188347
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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