GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ptsG in Paraburkholderia bryophila 376MFSha3.1

Align PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized)
to candidate H281DRAFT_01853 H281DRAFT_01853 PTS system D-glucose-specific IIB component, Glc family /PTS system D-glucose-specific IIC component, Glc family

Query= SwissProt::P37439
         (477 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_01853 H281DRAFT_01853 PTS
           system D-glucose-specific IIB component, Glc family /PTS
           system D-glucose-specific IIC component, Glc family
          Length = 596

 Score =  551 bits (1421), Expect = e-161
 Identities = 285/485 (58%), Positives = 364/485 (75%), Gaps = 9/485 (1%)

Query: 1   MFKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSANF-SWLPAVVSHVMAEAGGSVFANM 59
           +FK+AF  LQKVGKSLMLPV+VLP+AG+LLG+G+ +F  ++PA+V  +M  AG  +FAN+
Sbjct: 1   VFKHAFGVLQKVGKSLMLPVAVLPVAGLLLGLGATDFHGYVPAIVLALMKNAGDVIFANL 60

Query: 60  PLIFAIGVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIAAKHLADTGVL 119
           PLIFAIGVALGFT NDGVS +AA + Y +M  T+ V+A  V  +  + I       TGV 
Sbjct: 61  PLIFAIGVALGFTENDGVSGIAATIGYLVMTATLGVIAK-VEGIEPDMIMGIPSIQTGVF 119

Query: 120 GGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFVWPPIGTAI 179
           GGI++G +AA+MFNR+YRI LP YLGFFAGKRFVPI++ + +I  G +LS VWPPIG+AI
Sbjct: 120 GGILAGGLAAWMFNRYYRIALPAYLGFFAGKRFVPIVTAIGSIVLGAILSVVWPPIGSAI 179

Query: 180 QAFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTN-AAGQVFHGDIP 238
           +AFSQWAA  +P  A  +YGF+ER L+PFGLHHIWNVPF  + G + +   G+V HGDI 
Sbjct: 180 KAFSQWAAVSDPRTAATVYGFVERLLIPFGLHHIWNVPFFFEAGSFLDPTTGKVVHGDIT 239

Query: 239 RYMAGDPTAGMLSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITE 298
           R+ AGD TAG+L+G FLFKM+GLPAAAIAIWH AKPEN+  VGG+M+SAALTSFLTGITE
Sbjct: 240 RFFAGDRTAGILAGAFLFKMFGLPAAAIAIWHCAKPENKVAVGGMMVSAALTSFLTGITE 299

Query: 299 PIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIV--LSGN-SSKLW 355
           PIEF+F+FVAP+LY+IHA LA  A  +   LGMR G +FS G IDF++  L GN S+  W
Sbjct: 300 PIEFAFLFVAPVLYLIHACLAASAQFVANTLGMRMGFTFSQGGIDFLMFNLIGNKSTHAW 359

Query: 356 LFPIVGAGYAIVYYTVFRVLIKALDLKTPGREDTTDDAKAGATSEM---APALVAAFGGK 412
              I+G  YA++YY VFR +I   DLKTPGRED T +    +T+ +   +  LV AFGG+
Sbjct: 360 YVFILGPIYAVIYYGVFRFVITRFDLKTPGREDDTVETAKVSTAGVGGRSRELVLAFGGR 419

Query: 413 ENITNLDACITRLRVSVADVAKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDE 472
            NI +LDACITRLR+SV + A V++  LK LGAAGVV  G+GVQAIFG  S+N+KT+M E
Sbjct: 420 SNIDSLDACITRLRISVKNPALVNEGKLKALGAAGVVRVGNGVQAIFGPLSENMKTDMHE 479

Query: 473 YIRNS 477
           Y++ +
Sbjct: 480 YLKTA 484



 Score = 38.5 bits (88), Expect = 6e-07
 Identities = 27/74 (36%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 399 SEMAPALVAAFGGKENITNLDA-CITRLRVSVADVAKVDQAGLKKLGAAGVVVAGSG-VQ 456
           +E    + AA GG  NI  LDA   TRLRV + D +++D A LK  G        +G   
Sbjct: 522 AERVEKIRAALGGVANIQKLDALAATRLRVGLRDASQLDTAALKAAGVPATQTLTNGEFD 581

Query: 457 AIFGTKSDNLKTEM 470
            I G  + NL   M
Sbjct: 582 LIVGLDAPNLAGAM 595


Lambda     K      H
   0.325    0.140    0.421 

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: 891
Number of extensions: 47
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 477
Length of database: 596
Length adjustment: 35
Effective length of query: 442
Effective length of database: 561
Effective search space:   247962
Effective search space used:   247962
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