GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Phyllobacterium brassicacearum STM 196

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 WP_106712778.1 CU102_RS19520 sugar ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_003010955.1:WP_106712778.1
          Length = 505

 Score =  366 bits (939), Expect = e-105
 Identities = 209/500 (41%), Positives = 306/500 (61%), Gaps = 12/500 (2%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           LL    + KSF G RALD VDL +  GE+HALLGENGAGKSTLIK+L+  H  D G +  
Sbjct: 7   LLAARGICKSFIGFRALDAVDLTIRRGEIHALLGENGAGKSTLIKVLTGVHQPDLGVMEL 66

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122
            GQ +  RD  L+ QQLGI T+YQE NL P +SVA+N+++GR+P R G +D  R+   A+
Sbjct: 67  DGQPIHVRDT-LQAQQLGIGTVYQEVNLLPNMSVADNLFVGRQPMRFGFIDRRRMEKRAR 125

Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182
            LL+   L ++  + +   +VA QQ+V IA+A+ ++ R++I+DEPTA+L   E + L A 
Sbjct: 126 ELLSQYDLHIDVSSDLSRYSVAVQQLVAIARAVDMSGRILILDEPTASLDRHETEILFAT 185

Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR--- 239
           +  LK R + +++++H L +V  +CDR TV+R+G+   S   + +    +V LM+GR   
Sbjct: 186 LRRLKERGLGIVFITHFLDQVYEICDRVTVLRNGKVAGSELTSQLPKMQLVSLMLGRALA 245

Query: 240 HVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRT 299
            V    R+ R+ P       +G+     R  AP            GE++G+AGL+G+GRT
Sbjct: 246 AVTHNVRRDRQEPETKQFSFKGM--GRSRSVAP-----FDLDIGEGEVIGMAGLLGSGRT 298

Query: 300 DLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLS 359
           + ARL+FG D    G+  VD  P+R+RSP+DA+  G  L PEDRK  G   D S+R N+ 
Sbjct: 299 ETARLLFGIDSADTGQAAVDGVPVRIRSPQDAVALGFGLCPEDRKTDGIIGDLSVRENIV 358

Query: 360 LPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMAL 419
           L +L+A     + +  R +  L + + + L I+  D E  I  LSGGNQQKV+L R +A 
Sbjct: 359 L-ALQAQRGWFKRLPRRQQVALADKFVKALDIRTTDIEKPIKFLSGGNQQKVILARWLAT 417

Query: 420 TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGV 479
            P+ LI+DEPTRGID+GA AE+  +++ L D G+A++VISSE+ E++A S R+VV R+ V
Sbjct: 418 NPRFLILDEPTRGIDVGAHAEIIALINQLCDDGMALLVISSEIEEIVAYSTRVVVLRDRV 477

Query: 480 IVADLDAQTATEEGLMAYMA 499
              +L     T   +M  +A
Sbjct: 478 QRGELAGDDITTTKIMQKIA 497


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: 648
Number of extensions: 41
Number of successful extensions: 8
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: 505
Length adjustment: 34
Effective length of query: 481
Effective length of database: 471
Effective search space:   226551
Effective search space used:   226551
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 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