GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_01853
          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:

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