GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uhpT in Chromobacterium vaccinii MWU205

Align Glucose-6-P:Pi antiporter, Hpt (may also transport other organophosphates including C3 organophosphates) (characterized)
to candidate WP_046156002.1 VL52_RS04955 glycerol-3-phosphate transporter

Query= TCDB::Q9Z7N9
         (455 letters)



>NCBI__GCF_000971335.1:WP_046156002.1
          Length = 447

 Score =  337 bits (864), Expect = 5e-97
 Identities = 183/458 (39%), Positives = 271/458 (59%), Gaps = 25/458 (5%)

Query: 8   FQPPKHIKEIEDQEVVKKKYKYWRIRIFYSMFIGYIFYYFTRKSFTFAMPTLIADLGFDK 67
           F+P  H+  + D +     Y+  R +IF  +F+GY  YY  RK+F+ AMP L+ + GF +
Sbjct: 5   FKPAPHLPPLPDAQQ-HGLYRRLRWQIFLGIFLGYAGYYLVRKNFSLAMPYLV-EQGFSR 62

Query: 68  AQLGIIGSTLYFSYGISKFVSGVMSDQSNPRYFMAIGLMITGLTNIFFGM-----SSSIV 122
             LG   S +  +YG+SKF+ G +SD+SNPR F++ GL+++    +  G      SS  V
Sbjct: 63  GDLGFAMSGVAIAYGLSKFLMGAVSDRSNPRVFLSAGLVLSAAVFLLMGFAPWATSSVGV 122

Query: 123 LFALWWGLNGWFQGWGWPPCARLLTHWYAKSERGTWWSVWSTSHNIGGALIPILTGFIID 182
           +F L + LNGWFQG GWP C R + HW+++ ERG   S+W+ +HN+GG LI  L  FI+ 
Sbjct: 123 MFVLLF-LNGWFQGMGWPACGRTMVHWWSQKERGGVVSIWNCAHNVGGGLIGPL--FILG 179

Query: 183 ---YSGWRGAMYVPGILCIGMGLVLINRLRDTPQSLGLPPIEKYKRDPHHAHHEGKSASE 239
              ++ WR A YVP    IG+ +     +RDTPQS GLPP+E Y+ D            +
Sbjct: 180 MGWFNDWRAAFYVPAAAAIGVAVFAWLTMRDTPQSCGLPPVEAYRND---------YPED 230

Query: 240 GTEEIERELSTREILFTYVLTNQWLWFLAAASFFIYIVRMAVNDWSALFLIETKHYAAVK 299
            ++  E+EL+ REI   Y+L N+ LW++A A+ FIY++R  V DW+  +L E KH++  K
Sbjct: 231 YSDTHEQELTAREIFRKYILPNKLLWYIALANVFIYLLRYGVLDWAPTYLKEVKHFSVDK 290

Query: 300 ANFCVSLFEIGGLFGMLVAGWLSDKISKGNRGPMNVLFSLGLLFAILGMWFSRSHNQWWV 359
           +++   L+E  G+ G L+ GW+SDK+ +GNRG   V F   +  A +  W + + N   V
Sbjct: 291 SSWAYFLYEWAGIPGTLLCGWMSDKLFRGNRGATGVFFMALVTLATVVYWLNPAGNP-TV 349

Query: 360 DGTLLFVIGFFLYGPQMMIGLAAAELSHKKAAGTASGFTGWFAYFGATF-AGYPLGKVTD 418
           D   L  IGF +YGP M++GL A EL+ KKAAGTA+GFTG F Y G +  A   +G   D
Sbjct: 350 DMLALIAIGFLIYGPVMLVGLHALELAPKKAAGTAAGFTGLFGYLGGSVAANAAVGYTVD 409

Query: 419 VWGWKGFFIALL-ACASIALLLFLPTWNATEKNTRSKA 455
            +GW G F  L+ +C +  +LL L TW+  ++   + A
Sbjct: 410 HFGWDGGFALLIGSCVAAIVLLALTTWHGHQQGKLASA 447


Lambda     K      H
   0.327    0.141    0.476 

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: 825
Number of extensions: 48
Number of successful extensions: 6
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: 455
Length of database: 447
Length adjustment: 33
Effective length of query: 422
Effective length of database: 414
Effective search space:   174708
Effective search space used:   174708
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