GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uhpT in Bacteroides thetaiotaomicron VPI-5482

Align Glucose-6-P:Pi antiporter, Hpt (may also transport other organophosphates including C3 organophosphates) (characterized)
to candidate 349724 BT0196 putative hexose phosphate transport protein (NCBI ptt file)

Query= TCDB::Q9Z7N9
         (455 letters)



>FitnessBrowser__Btheta:349724
          Length = 448

 Score =  227 bits (579), Expect = 5e-64
 Identities = 138/440 (31%), Positives = 221/440 (50%), Gaps = 32/440 (7%)

Query: 24  KKKYKYWRIRIFYSMFIGYIFYYFTRKSFTFAMPTLIADLGFDKAQLGIIGSTLYFSYGI 83
           K++ KY +   F S   GY  YY  R S       ++ +  F + +LGIIGS L+F+Y +
Sbjct: 27  KRRLKYLQWSTFLSATFGYGMYYVCRLSLNVVKKPIVDEGIFSETELGIIGSVLFFTYAV 86

Query: 84  SKFVSGVMSDQSNPRYFMAIGLMITGLTNIFFGMSSSIVLFALWWGLNGWFQGWGWPPCA 143
            KF +G ++D+SN   FM  GL++T L N+  G S S +LFA+ WG++GWFQ  G   C 
Sbjct: 87  GKFTNGFLADRSNINRFMTTGLLVTALINLCLGFSHSFILFAVLWGVSGWFQSMGAASCV 146

Query: 144 RLLTHWYAKSERGTWWSVWSTSHNIGGALIPILTGFIIDYSGWRGAMYVPGILCIGMGLV 203
             L+ W+   ERG+++  WS SHNIG AL  I+   I+   GWR   +  G++ +   L+
Sbjct: 147 VGLSRWFTDKERGSYYGFWSASHNIGEALTFIIVASIVSVCGWRYGFFGAGMVGLLGALI 206

Query: 204 LINRLRDTPQSLGLPPIEKYKRDPHHAHHEGKSASEGTEEIERELSTREILFTYVLTNQW 263
           +     D+P+S G PP+   K        +  SASE T+  + +          VLT   
Sbjct: 207 VWRFFHDSPESKGFPPVNVPK------EKKTMSASETTDFNKAQ--------RQVLTMPA 252

Query: 264 LWFLAAASFFIYIVRMAVNDWSALFLIETKHYAAVKANFCVSLFEIGGLFGMLVAGWLSD 323
           +W LA +S F+YI R AVN W   +L   K Y+ + A+F +S+  + G+ G + +G +SD
Sbjct: 253 IWILALSSAFMYISRYAVNSWGVFYLEAQKGYSTLDASFIISISSVCGIIGTMFSGVISD 312

Query: 324 KISKGNRGPMNVLFSLGLLFAILGMWFSRSHNQWWVDGTLLFVIGFFLYGPQMMI----G 379
           K+  G R    ++F L  + A L ++       +W+D   + + G    G  ++I    G
Sbjct: 313 KLFGGRRNVPALIFGLTNVLA-LCLFLLVPGVHFWLDAVAMILFGL---GIGVLICFLGG 368

Query: 380 LAAAELSHKKAAGTASGFTGWFAYFGATFAGYPLGKV----------TDVWGWKGFFIAL 429
           L A +++ + A+G A G  G  +Y GA       G +           +V+ +       
Sbjct: 369 LMAVDIAPRNASGAALGVVGIASYIGAGLQDVMSGVLIEGHKTIRSGVEVYDFTYINWFW 428

Query: 430 LACASIALLLFLPTWNATEK 449
           +  A +++   L  WNA +K
Sbjct: 429 IGSAILSVFFALWVWNAKQK 448


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: 800
Number of extensions: 50
Number of successful extensions: 4
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: 448
Length adjustment: 33
Effective length of query: 422
Effective length of database: 415
Effective search space:   175130
Effective search space used:   175130
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 17 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