GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG in Shewanella oneidensis MR-1

Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)

Query= BRENDA::P69786
         (477 letters)



>FitnessBrowser__MR1:200788
          Length = 499

 Score =  424 bits (1091), Expect = e-123
 Identities = 205/471 (43%), Positives = 307/471 (65%), Gaps = 8/471 (1%)

Query: 6   FANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPLIFAI 65
           F   Q++ ++L++P+++LP AG++LG+  +   ++P V++ +M   G  +FA MP++FA+
Sbjct: 25  FKFAQRLSQALLIPIAILPAAGVMLGLTVSPIPFMPEVLNVLMLAVGKLIFAIMPILFAV 84

Query: 66  GVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLGGIISG 125
            VA+GF  + G++A  AV  YG+M  T+A +A L   LP + +      DTG+ GG++ G
Sbjct: 85  AVAIGFCRDQGIAAFTAVFGYGVMTATLAALADLY-QLPTQLVLGMETLDTGIAGGMLIG 143

Query: 126 AIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQTFSQW 185
            +  +       I+LP    FF G+R   ++    A+  G VL+ IWP +   I+  S W
Sbjct: 144 GVTCFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYVLAHIWPSLSLLIERVSDW 203

Query: 186 AAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYMAGDP 245
           A YQ P +AFG+YG +ER L+P GLHHIWN PF +++G+Y     +V  G++ RY+AGDP
Sbjct: 204 AVYQKPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQYQLQDAEVVRGEVARYLAGDP 263

Query: 246 TAGKLSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSFM 305
            AG L+GG+L KM+GLPAAA+AIW  A    R +V GIM+SAA  S+LTG+TEPIEF+FM
Sbjct: 264 QAGNLAGGYLIKMWGLPAAALAIWRCADNSERNRVAGIMLSAAAASWLTGVTEPIEFAFM 323

Query: 306 FVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIVGIGYA 365
           FVAP+L++IH +L+GLA+ +CI+L +     FSHGL+DF +L   S     F ++G   A
Sbjct: 324 FVAPLLFLIHVMLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFAVLGPLTA 383

Query: 366 IVYYTIFRVLIKALDLKTPGR--EDATEDAKATGTSEMAPALVAAFGGKENITNLDACIT 423
           ++YY +FR  I A +LKTPGR   D T+     G+ E   A++AA GG++NI  L+AC+T
Sbjct: 384 VIYYILFRGSILAFNLKTPGRLQSDGTK-----GSKESLRAIIAALGGRDNIVELNACLT 438

Query: 424 RLRVSVADVSKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYI 474
           RLR+SV     V++  L +LGA GV+V G GVQ ++GTK++ L+  +  Y+
Sbjct: 439 RLRLSVHSPELVNKVRLSQLGAKGVIVMGKGVQIVYGTKAETLRKVLQRYL 489


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: 656
Number of extensions: 28
Number of successful extensions: 3
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: 499
Length adjustment: 34
Effective length of query: 443
Effective length of database: 465
Effective search space:   205995
Effective search space used:   205995
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: 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:

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