Alignments for a candidate for treEIIA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Burkholderia phytofirmans PsJN

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate BPHYT_RS02740 BPHYT_RS02740 PTS glucose transporter subunit IIA

Query= reanno::WCS417:GFF4500
         (838 letters)



>FitnessBrowser__BFirm:BPHYT_RS02740
          Length = 854

 Score =  603 bits (1554), Expect = e-176
 Identities = 363/843 (43%), Positives = 504/843 (59%), Gaps = 30/843 (3%)

Query: 9   LLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSITD 68
           LLAP++G ++ L  VPDPVFS  + GDG+ +DP    L AP    ++++  +GHAV++  
Sbjct: 10  LLAPMTGPVVPLANVPDPVFSGGMFGDGIGVDPLEGRLVAPCDATVTHLARTGHAVTLAT 69

Query: 69  DNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLMLVV 128
             G ++L+HIG+DTV L G+GF  +V +G  V AG  LIEFD D VALNA SL++++ + 
Sbjct: 70  AEGAEILLHIGIDTVELNGKGFAPMVAQGAHVRAGDVLIEFDQDQVALNAPSLVSVIAIA 129

Query: 129 SGEPFSLLA---DGLVETGQ-PLLQL-SPSGAVEAVDEEEGDALFSKP----LTLPNANG 179
           + + F ++     GL++ G+ PLL L +  GA      +      ++     +TL +A G
Sbjct: 130 NSDAFEIVERVQGGLLKAGETPLLVLRARDGAAAEASRQLSSTNVTEEARQQVTLVHAGG 189

Query: 180 LHARPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAA 239
           LHARPAA   +AA+GF+A + +  + + A  +S+V ++ L   +G T+++   G  A AA
Sbjct: 190 LHARPAARAREAARGFDARVEVRYEGRKAAIESVVGLLGLGAGEGATVELLGMGPQAAAA 249

Query: 240 IKALV-ALLAEGCGE-----------AVVNVAEPVATQSSATLLRGVCASPGSAFGQVVQ 287
           + A+   L  E  GE           A   VA P     +   L GVCA+PG A G++V+
Sbjct: 250 VAAIANELTREAHGEVEEKPARQSSPAPQAVARPAGETLAPNTLAGVCAAPGVAVGKLVR 309

Query: 288 VTDPELVITEQGTG-GATERAALTRGLLAANEALQV-LQDKAAGSA--QAEIFRAHQELL 343
             D ++   E+  G  A E   L + +   +  L   ++D +   A  +A IF  H+ LL
Sbjct: 310 WDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDASQRGAVGEAGIFSVHRVLL 369

Query: 344 EDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLI 403
           EDPTLL+ A  L+  GKSA FAW  A  A + +   + +AL+AERAADL D+ +RVL+ +
Sbjct: 370 EDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRAL 429

Query: 404 LGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAI 463
                +A  LPE A+L AE+ TPS  ++LD  +V   V   GGATSH AILAR  G+PA+
Sbjct: 430 GYTSATARTLPEEAVLAAEEFTPSDLSTLDRSRVTALVMARGGATSHAAILARQAGIPAL 489

Query: 464 CGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQ--LEAARKHQVLRHQRDVAQASLP 521
             V   + A+  G QV+++A  G L   P   ++E+  LE  R   V    R  +Q +  
Sbjct: 490 VAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVERARLERTRLADVREANRRTSQQA-- 547

Query: 522 ATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAI 581
           A T DG  +EV AN+A+L + + A+  G + VGLLR+E L++ R  AP+ +E   +Y AI
Sbjct: 548 AVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQAI 607

Query: 582 ARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILA 641
             AL + R  ++RTLDVG DK + Y+ +  E NP LGLRGIRL   RP LL +Q R +LA
Sbjct: 608 VDAL-SGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLA 666

Query: 642 SAGFARLHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAP 701
                 + I+LPMV+ + EL   RK ++E A  LG TE  ++G+MIEVPSAAL+AD  A 
Sbjct: 667 VQPLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIEVPSAALLADQLAQ 726

Query: 702 HVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGA 761
           H DF SIGTNDLTQYTLAMDR    LA QAD  HPAVLRLIA TV+ A  HGKWVGVCGA
Sbjct: 727 HADFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGA 786

Query: 762 LASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREA 821
           LA + LA+P+L+GLGV ELSV    +P IKA VR LD   C+  A+  L LE A  VR A
Sbjct: 787 LAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVRAA 846

Query: 822 LRQ 824
            R+
Sbjct: 847 SRE 849


Lambda     K      H
   0.318    0.133    0.371 

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: 1571
Number of extensions: 69
Number of successful extensions: 6
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: 838
Length of database: 854
Length adjustment: 42
Effective length of query: 796
Effective length of database: 812
Effective search space:   646352
Effective search space used:   646352
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources