GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolT in Pedobacter sp. GW460-11-11-14-LB5

Align Major myo-inositol transporter, IolT1, of 456 aas (characterized)
to candidate CA265_RS01275 CA265_RS01275 hypothetical protein

Query= TCDB::E1WAV3
         (456 letters)



>FitnessBrowser__Pedo557:CA265_RS01275
          Length = 462

 Score =  279 bits (714), Expect = 1e-79
 Identities = 156/446 (34%), Positives = 258/446 (57%), Gaps = 21/446 (4%)

Query: 1   MGGILFGYDTAVISGAIGSLTSYFHLSPAETGWAVSCVVVGCVIGSFSAGYLSKRFGRKK 60
           +GG LFG+D AV+SG I  L S + LS A+ G  VSC ++GC++G   +GYLS + GR+K
Sbjct: 19  LGGFLFGFDMAVVSGIIEPLKSQYGLSSAQEGLFVSCALLGCIVGVSFSGYLSDKVGRRK 78

Query: 61  SLMVSALLFTISAVGTSLSYTFTHFVIYRIIGGLAVGLAATVSPMYMSEVSPKNMRGRAL 120
            L ++A+LF +SAVG + S  +   + +R++ G+ VG+A+ VSP+Y+SEV+P   RGR +
Sbjct: 79  VLFLAAILFLVSAVGFAFSVAYPVLIFFRVLAGMGVGVASNVSPLYISEVAPSQKRGRLV 138

Query: 121 SMQQFAIVFGQILIFYVN----YKIASIAADT------WL-IELGWRYMFAAGIIPCILF 169
              Q AI  G IL  Y++     + A++ A        WL +E  WR MF  G++P   F
Sbjct: 139 VFYQLAITIG-ILAAYISNLFLQRYATVHAGAGEGILHWLFVENVWRGMFIVGVVPAAAF 197

Query: 170 CILVFLIPESPRWMMMIGREEETLKILTKISNEEHARHLLADIKTSLQNDQLNAHQKLNY 229
           C+L+ ++PESPRW++  GR EE L  L KI+  E  R  L  IK  + + +   +++L  
Sbjct: 198 CLLLLIVPESPRWLVQYGRNEEALNTLIKINGAETGRLELDSIK-EMASQKSGGYKELMR 256

Query: 230 RDGNVRFILILGCMIAMLQQVTGVNVMMYYAPIVLKDVTGSAQEALFQTIWIGVIQLIGS 289
               +  +L L  ++  L Q +G+N +++Y P +LK       +ALF  + +G   ++ +
Sbjct: 257 LP--LSKLLALATILTALSQFSGINGVIFYGPTILKSAGIVTSDALFYQVILGSANVLFT 314

Query: 290 IIGAMIMDKMGRLSLMRKGTIGSIIGLLLTSWALYSQATGYFALFGMLFFMIFYALSWGV 349
            I    +D  GR  L   G++ +   L LT +      TG+F LF ++ F++F+A S G 
Sbjct: 315 FIAISKVDTWGRRPLYIIGSLCAAGALALTGFCFLMDITGWFMLFSIILFLLFFAFSLGP 374

Query: 350 GAWVLISEIFPNRMRSQGMSISVGFMWMANFLVSQFFPMINENPYLLSHFHGAFPMWIFA 409
             +V+ +EIFP  +R   +S+ +  MW+++++V+  FP++ +   + + F      +IF+
Sbjct: 375 LKFVISTEIFPTHIRGTALSMCIMTMWVSDWVVNMLFPIMRDGLGIATTF------FIFS 428

Query: 410 ICCIFSYFFICRYLPETKGISLEKME 435
             CI S+ +  + L ETKG SLE++E
Sbjct: 429 FFCILSFLYAKKKLFETKGKSLEEIE 454


Lambda     K      H
   0.329    0.141    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: 636
Number of extensions: 35
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: 456
Length of database: 462
Length adjustment: 33
Effective length of query: 423
Effective length of database: 429
Effective search space:   181467
Effective search space used:   181467
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 (21.8 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