GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malEIICBA in Burkholderia phytofirmans PsJN

Align PTS system, IIABC components (characterized, see rationale)
to candidate BPHYT_RS02745 BPHYT_RS02745 PTS system N-acetylglucosamine-specific transporter subunit IIBC

Query= uniprot:Q836Y6
         (722 letters)



>FitnessBrowser__BFirm:BPHYT_RS02745
          Length = 591

 Score =  231 bits (589), Expect = 8e-65
 Identities = 181/546 (33%), Positives = 260/546 (47%), Gaps = 89/546 (16%)

Query: 11  QKFGKALMVVVAVMPAAGLMISIGKSLPLIDPNLGLLVTTGGVLESIGWAIIGNLHLLFA 70
           Q+ G+ALM+ +AV+P AGL++ +G+       N+ ++   GG       AI  NL LLFA
Sbjct: 10  QRLGRALMLPIAVLPVAGLLLRLGQPDVF---NIKMIADAGG-------AIFDNLPLLFA 59

Query: 71  LAIGGSWAKDRAGGAFAAGISFVLINRITGAIFGVTNEMLADEQAFTHTLFGTKIMVKGF 130
           + +   +AKD  G A  AG    LI     A+    N+ L                    
Sbjct: 60  IGVAVGFAKDNNGVAGLAGAIGYLIEV---AVMKDINDKL-------------------- 96

Query: 131 FTSVLEAPALNMGVFVGIIAGFVGAMAYNKYYNYRKLPDALSFFNGKRFVPFVVILWSTI 190
                     NMGV  GI+AG V  + YN+Y +  KLPD L+FF GKRFVP V  +   +
Sbjct: 97  ----------NMGVLSGIVAGIVAGLLYNRYKDI-KLPDYLAFFGGKRFVPIVTGVVCLV 145

Query: 191 VSIALALIWPNIQAGINNFGLWIAQSQDSAPILAPFLYGTLERLLLPFGLHHMLTIPINY 250
           + IA   +W  +QA I+  G W+     +A  L  F++G L RLLL  GLHH+L     +
Sbjct: 146 LGIAFGYVWQPVQAVIDTAGHWLT----TAGALGAFVFGVLNRLLLVTGLHHILNSLTWF 201

Query: 251 TQLGGTYEILSGAQAGTQVFGQDPLWLAWATDLVNLKGAGDMSKYQFVLENWTPARFKVG 310
             + GT+    GA                          GD+  ++F   + T   F  G
Sbjct: 202 --VFGTFTPPGGAAV-----------------------TGDL--HRFFAGDPTAGTFMTG 234

Query: 311 QMIGSSGILMGMALAMYRNVDADKKAKYKSMYFSAALAVFLTGVTEPLEFMFMFAAVPLY 370
                   L    LAM+     +++A    + FS AL  FLTGVTEP+EF FMF A  LY
Sbjct: 235 FFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLY 294

Query: 371 VIYAVIQGAAFAMADILPLRV---HSFGNIELLTRTPLAIKAGLGGDLINFVLMVIIFGV 427
           VI+A++ G + A+   L + +    S G I+ +    L+ + G     I  V MV+ +G 
Sbjct: 295 VIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTR-GWWAIPIGLVYMVVYYG- 352

Query: 428 VTYFLANFLIKKFNYATPGRNGNYDNDNSEEIASGAAGS---GVVDQQIAQIVYLLGGKQ 484
               L  F I+KFN ATPGR     ++  +  A+G   S   G    +  + +  LGG  
Sbjct: 353 ----LFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGAS 408

Query: 485 NIKEVDACMTRLRVSVKDREKVGSEEAWKRAGAMGLIVK-DNGVQAVYGPKADVLKSDIE 543
           N+  VDAC TRLR+SV D  KV SE   K  GA G++ +    VQ + GP+AD++  +I 
Sbjct: 409 NLSVVDACTTRLRLSVVDSNKV-SENELKTIGARGVLKRGSTNVQVIIGPEADIIADEIR 467

Query: 544 DLLASG 549
            ++A G
Sbjct: 468 TVIAQG 473



 Score = 34.3 bits (77), Expect = 2e-05
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 7/72 (9%)

Query: 460 ASGAAGSGVVDQQIAQIVYLLGGKQNIKEVDA-CMTRLRVSVK-----DREKVGS-EEAW 512
           AS A GSG +D    + + + GG  N+  +DA   TRLR+ V+     DR+++ + + AW
Sbjct: 496 ASVAQGSGPLDPDPLRWLAVFGGAGNVLSLDAIAATRLRIVVRDPSAVDRQRLATLDTAW 555

Query: 513 KRAGAMGLIVKD 524
             A    ++V D
Sbjct: 556 ISADTFHIVVGD 567


Lambda     K      H
   0.322    0.138    0.404 

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: 1075
Number of extensions: 63
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 722
Length of database: 591
Length adjustment: 38
Effective length of query: 684
Effective length of database: 553
Effective search space:   378252
Effective search space used:   378252
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 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