GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ptsG in Shewanella amazonensis SB2B

Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)

Query= BRENDA::P69786
         (477 letters)



>lcl|FitnessBrowser__SB2B:6936959 Sama_1133 PTS system,
           glucose-specific IIBC component (RefSeq)
          Length = 485

 Score =  435 bits (1118), Expect = e-126
 Identities = 210/469 (44%), Positives = 307/469 (65%), Gaps = 7/469 (1%)

Query: 6   FANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPLIFAI 65
           F   Q++ ++L++P+++LP AG+++G+ +    ++P V + +M   G  +F  MP++FAI
Sbjct: 20  FRFAQRLSQTLLIPIAILPAAGVMIGIATNPLPFIPDVANVLMLSVGKLIFDIMPMLFAI 79

Query: 66  GVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLGGIISG 125
            VA+GF  + G++A +A   YG+++ T+A  A  V HLP+  +      DTG+ GG++ G
Sbjct: 80  AVAIGFCRDQGIAAFSAAFGYGVLLSTLAAAAK-VYHLPSHIVWGTPTIDTGIAGGMLVG 138

Query: 126 AIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQTFSQW 185
            I         +++LP    FF G+R  P+I     +   V+L+FIWPP+  +I+  S W
Sbjct: 139 GITCVAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLVMLLAVMLAFIWPPLALSIERLSDW 198

Query: 186 AAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYMAGDP 245
           A YQ P +AFG YG +ER L+P GLHHIWN PF +++G+Y +  G++  G++ RY AGDP
Sbjct: 199 AVYQEPAIAFGFYGMVERLLLPLGLHHIWNAPFYLEVGQYAHD-GEIVRGEMARYFAGDP 257

Query: 246 TAGKLSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSFM 305
           +AG L+GG+L KM+GLPAAA+AIW  A    R +V G+M+SAA  S+LTG+TEPIEF+F+
Sbjct: 258 SAGNLAGGYLIKMWGLPAAALAIWRCADRNQRNRVAGVMLSAATASWLTGVTEPIEFAFL 317

Query: 306 FVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIVGIGYA 365
           FVAP+LY+ HA+L GLA+ I ILL M     FSHGL+DF++L   SS       +G    
Sbjct: 318 FVAPLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLFPQSSNTHWIWFLGPLTF 377

Query: 366 IVYYTIFRVLIKALDLKTPGREDATEDAKATGTSEMAPALVAAFGGKENITNLDACITRL 425
           ++YY +FR  I A +LKTPGR +A      TG      A+V+A GG  NI +L AC+TRL
Sbjct: 378 VIYYILFRASILAFNLKTPGRFEAD-----TGQKRNLIAIVSALGGGGNIADLSACLTRL 432

Query: 426 RVSVADVSKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYI 474
           R+SVAD S+VD+  L  LGA GV+V GSGVQ +FGTK++ L+  +  Y+
Sbjct: 433 RISVADPSQVDRQRLMSLGAKGVIVVGSGVQLVFGTKAETLRKLLQRYL 481


Lambda     K      H
   0.325    0.140    0.422 

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: 690
Number of extensions: 30
Number of successful extensions: 4
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: 477
Length of database: 485
Length adjustment: 34
Effective length of query: 443
Effective length of database: 451
Effective search space:   199793
Effective search space used:   199793
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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