GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malEIIA in Escherichia coli BW25113

Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate 15223 b1101 fused glucose-specific PTS enzymes: IIB component/IIC component (NCBI)

Query= CharProtDB::CH_001857
         (699 letters)



>lcl|FitnessBrowser__Keio:15223 b1101 fused glucose-specific PTS
           enzymes: IIB component/IIC component (NCBI)
          Length = 477

 Score =  441 bits (1134), Expect = e-128
 Identities = 243/514 (47%), Positives = 334/514 (64%), 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+ +AA++ Y +M  +M+ V      +P++ +
Sbjct: 49  AEAGGSVFANMPLIFAIGVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEI 108

Query: 121 ERAKFFTENHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRF 180
                    H A           TGV GGII G +AA +FNRFY I+LP+YLGFFAGKRF
Sbjct: 109 ------ASKHLA----------DTGVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRF 152

Query: 181 VPIVTSISALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHH 240
           VPI++ ++A+  G+++  IWPPI   +  FS      NP +A  I+G IER L+PFGLHH
Sbjct: 153 VPIISGLAAIFTGVVLSFIWPPIGSAIQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHH 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+G A++YY  FR  I+  +LKTP
Sbjct: 327 ILLGMRDGTSFSHGLIDFIV--LSGNSSKLWLFPIVGIGYAIVYYTIFRVLIKALDLKTP 384

Query: 421 GREDAAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKVDKDRL 480
           GREDA E+  A G      ++   ++ A G +ENI +LDACITRLRV+V D  KVD+  L
Sbjct: 385 GREDATEDAKATG----TSEMAPALVAAFGGKENITNLDACITRLRVSVADVSKVDQAGL 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: 938
Number of extensions: 44
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 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