GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ptsG in Shewanella loihica PV-4

Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate 5210198 Shew_2641 PTS system, glucose-like IIB subunint (RefSeq)

Query= BRENDA::P69786
         (477 letters)



>lcl|FitnessBrowser__PV4:5210198 Shew_2641 PTS system, glucose-like
           IIB subunint (RefSeq)
          Length = 490

 Score =  416 bits (1070), Expect = e-121
 Identities = 201/472 (42%), Positives = 305/472 (64%), Gaps = 7/472 (1%)

Query: 6   FANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPLIFAI 65
           F   Q++ ++L+LP+++LP AG+++G+ +    ++ A ++ +M   G  VF+ MP++FA+
Sbjct: 24  FKFAQRLSQALLLPIAILPAAGVMIGLATNPIPFISADLATLMWTVGNLVFSMMPMLFAV 83

Query: 66  GVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLGGIISG 125
            +A+GF  + G++A +AV  YG+   +++ +A  + HLP E I  +   DTG+ GG++ G
Sbjct: 84  TIAIGFCRDQGIAAFSAVFGYGVFFSSLSALAK-IYHLPTEMILGQATIDTGIAGGMMVG 142

Query: 126 AIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQTFSQW 185
           A    +     RI+LP    FF G+R  P++    AI    +   +WP + + I+  S W
Sbjct: 143 AFTCLVVKHSERIRLPAVFSFFEGRRSAPLLMLPMAILLAYLFLLLWPLLSNWIEQISNW 202

Query: 186 AAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYMAGDP 245
           A YQ P  AF +YG +ER L+P GLHHIWN PF +++G+Y N    V  G++ RY+AGDP
Sbjct: 203 AVYQEPASAFAVYGMVERLLIPLGLHHIWNAPFYLEMGQYFNGDEWV-RGEVARYLAGDP 261

Query: 246 TAGKLSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSFM 305
            AG L+GG+L KM+GLPAAA+AIW  A    R +V GIM+SAA   +LTG+TEPIEF+FM
Sbjct: 262 QAGNLAGGYLIKMWGLPAAALAIWRCADKHERNRVAGIMLSAATACWLTGVTEPIEFAFM 321

Query: 306 FVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIVGIGYA 365
           FVAP+L+I+HA++ G+A+ + I L +     FSHGL+DF +L G S  +  F I+G   A
Sbjct: 322 FVAPLLFILHALMTGIAYAVTISLDIHHSVVFSHGLVDFSLLLGQSRNVEWFLILGPLTA 381

Query: 366 IVYYTIFRVLIKALDLKTPGREDATEDAKATGTSEMAPALVAAFGGKENITNLDACITRL 425
           ++YY +FR  I A +LKTPGR +A    +A   S     ++ A GG++NI  L AC+TRL
Sbjct: 382 VIYYLVFRGAILAFNLKTPGRMEAGSGQRAGLIS-----MITALGGQDNINELTACLTRL 436

Query: 426 RVSVADVSKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYIRNH 477
           R+SV     VD+A L KLGA GVV+ G+GVQ ++GTK+++++  +  Y+  H
Sbjct: 437 RISVKHAELVDKAQLNKLGAKGVVLVGNGVQLVYGTKAESIRRLLQRYLDRH 488


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: 641
Number of extensions: 29
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: 490
Length adjustment: 34
Effective length of query: 443
Effective length of database: 456
Effective search space:   202008
Effective search space used:   202008
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 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