GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iatA in Klebsiella michiganensis M5al

Align Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter

Query= TCDB::B8H229
         (515 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS14860 BWI76_RS14860 ABC
           transporter
          Length = 510

 Score =  377 bits (967), Expect = e-109
 Identities = 215/504 (42%), Positives = 321/504 (63%), Gaps = 18/504 (3%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           LL +  +SK +    AL+ V   +  GEVHAL+GENGAGKSTL+KILS     D+G +  
Sbjct: 9   LLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFI 68

Query: 63  AGQVLD---PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRL-GLVDWSRLR 118
            GQ +D   PRDA    ++ GIA I+QE N  P+++VAEN++LG+EP    G++D  R+ 
Sbjct: 69  DGQAIDIRTPRDA----RKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRMH 124

Query: 119 ADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDR 178
            +A+  LN +   ++P AP+  L++  QQMVEIA+A++ NA+++++DEPTAALS  E  +
Sbjct: 125 REAKEKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQ 184

Query: 179 LHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVG 238
           L+ +IA ++   V ++Y+SHR+ EV  + +R TV RDG ++ + ++ +V   D+VR+MVG
Sbjct: 185 LYRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMVG 244

Query: 239 RHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGR 298
           R +    +   R PG V+L+V  +  +A   + P     VSF    GE+V ++GLVG+GR
Sbjct: 245 RQIVDLYQHEPRTPGDVLLEVRDLAGSA---TGP-----VSFEVSAGEVVSMSGLVGSGR 296

Query: 299 TDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNL 358
           T++ARL+FGADP + G V +  +  +   P  AI  GI +V EDRK QG FL HS+  N+
Sbjct: 297 TEVARLLFGADPRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNI 356

Query: 359 SLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMA 418
            + SL    A G  V  +  R  V    ++LR++    E  +  LSGGNQQK  L R + 
Sbjct: 357 DISSLDNFVA-GGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLL 415

Query: 419 LTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREG 478
              ++LI+DEPTRG+DIGAK E+++++  LA  G A++VISS+L E + +SDR++V R G
Sbjct: 416 RDSRLLILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGG 475

Query: 479 VIVADLDAQTATEEGLMAYMATGT 502
            IV  L + +ATEE +M + ATGT
Sbjct: 476 RIVHQLPSCSATEEEVMLH-ATGT 498


Lambda     K      H
   0.320    0.136    0.380 

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: 703
Number of extensions: 27
Number of successful extensions: 9
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: 515
Length of database: 510
Length adjustment: 35
Effective length of query: 480
Effective length of database: 475
Effective search space:   228000
Effective search space used:   228000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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