GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG-crr in Klebsiella michiganensis M5al

Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate BWI76_RS11130 BWI76_RS11130 PTS glucose transporter subunit IIBC

Query= CharProtDB::CH_001857
         (699 letters)



>FitnessBrowser__Koxy:BWI76_RS11130
          Length = 477

 Score =  440 bits (1132), Expect = e-128
 Identities = 243/514 (47%), Positives = 335/514 (65%), Gaps = 40/514 (7%)

Query: 1   MFKALFGVLQKIGRALMLPVAILPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVM 60
           MFK  F  LQK+G++LMLPV++LP AGILL +G+A  N   +  +          V+ VM
Sbjct: 1   MFKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSA--NFSWLPAV----------VSHVM 48

Query: 61  ESAGQIVFDNLPLLFAVGVAIGLANGDGVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSV 120
             AG  VF N+PL+FA+GVA+G  N DGV+ +A+++ Y +M  +MS V      +P++ +
Sbjct: 49  AEAGGSVFANMPLIFAIGVALGFTNNDGVSALASVVAYGIMVKTMSVVAPLVLHLPAEEI 108

Query: 121 ERAKFFTENHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRF 180
             AK   +               TGV GGII G +AA +FNRFY I+LP+YLGFFAGKRF
Sbjct: 109 A-AKHLAD---------------TGVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRF 152

Query: 181 VPIVTSISALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHH 240
           VPI++ ++A+  G+I+  IWPPI   +  FS      NP +A  I+G IER L+PFGLHH
Sbjct: 153 VPIISGLAAIFTGVILSFIWPPIGTAIQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHH 212

Query: 241 IFYSPFWYEFFSYKSAAGEIIRGDQRIFMAQIKDGVQLTAGTFMTGKYPFMMFGLPAAAL 300
           I+  PF  +   Y +AAG++  GD   +MA        TAG  ++G + F M+GLPAAA+
Sbjct: 213 IWNVPFQMQIGEYTNAAGQVFHGDIPRYMAG-----DPTAGK-LSGGFLFKMYGLPAAAI 266

Query: 301 AIYHEAKPQNKKLVAGIMGSAALTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSFMVM 360
           AI+H AKP+N+  V GIM SAALTSFLTGITEP+EFSF+FVAP+L+ IH + AGL+F + 
Sbjct: 267 AIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSFMFVAPILYIIHAILAGLAFPIC 326

Query: 361 QLLNVKIGMTFSGGLIDYFLFGILPNRTAWWLVIPVGLGLAVIYYFGFRFAIRKFNLKTP 420
            LL ++ G +FS GLID+ +  +  N +  WL   VG+  A++YY  FR  I+  +LKTP
Sbjct: 327 ILLGMRDGTSFSHGLIDFIV--LSGNSSKLWLFPIVGICYAIVYYVVFRVLIKALDLKTP 384

Query: 421 GREDAAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKVDKDRL 480
           GREDA E++    K G   ++   ++ A G +ENI +LDACITRLRV+V D  KVD+  L
Sbjct: 385 GREDATEDS----KAGATSEMAPALIAAFGGKENITNLDACITRLRVSVADVAKVDQAGL 440

Query: 481 KQLGASGVLEVGNNIQAIFGPRSDGLKTQMQDII 514
           K+LGA+GV+  G+ +QAIFG +SD LKT+M + I
Sbjct: 441 KKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYI 474


Lambda     K      H
   0.323    0.141    0.412 

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: 925
Number of extensions: 41
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: 699
Length of database: 477
Length adjustment: 36
Effective length of query: 663
Effective length of database: 441
Effective search space:   292383
Effective search space used:   292383
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 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