Alignments for a candidate for malEIICBA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for malEIICBA in Paraburkholderia bryophila 376MFSha3.1

Align PTS system, IIABC components (characterized, see rationale)
to candidate H281DRAFT_01976 H281DRAFT_01976 PTS system N-acetylglucosamine-specific IIB component, Glc family /PTS system N-acetylglucosamine-specific IIC component, Glc family

Query= uniprot:Q836Y6
         (722 letters)



>FitnessBrowser__Burk376:H281DRAFT_01976
          Length = 599

 Score =  228 bits (581), Expect = 7e-64
 Identities = 195/616 (31%), Positives = 281/616 (45%), Gaps = 107/616 (17%)

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-KLPDYLAFFGGKRFVPIVTGVVCLA 145

Query: 191 VSIALALIWPNIQAGINNFGLWIAQSQDSAPILAPFLYGTLERLLLPFGLHHMLTIPINY 250
           + I    +W  +Q+ I+  G W+     +A  L  F++G L RLLL  GLHH+L     +
Sbjct: 146 LGILFGYVWQPVQSVIDTAGHWLT----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 FFPVMMFGLPAACLAMFHEAPKERRAIVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLY 294

Query: 371 VIYAVIQGAAFAMADILPLRV---HSFGNIELLTRTPLAIKAGLGGDLINFVLMVIIFGV 427
           VI+A++ G A A+   L + +    S G I+ +    L+ K  L       + + I++ V
Sbjct: 295 VIHALLTGLALAICSALGIHLGFTFSAGAIDYVLNYGLSTKGWLA------IPVGIVYAV 348

Query: 428 VTYFLANFLIKKFNYATPGRNGNYDNDNSEEIASGAAGS---GVVDQQIAQIVYLLGGKQ 484
           V Y L  F I+KFN ATPGR     ++  +  A+G   S   G    +  + +  LGG  
Sbjct: 349 VYYGLFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGAAVPRAQRYIAALGGAA 408

Query: 485 NIKEVDACMTRLRVSVKDREKVGSEEAWKRAGAMGLIVKD-NGVQAVYGPKADVLKSDIE 543
           N+  VDAC TRLR+SV D  KV SE   K  GA G++ +    VQ + GP+AD++  +I 
Sbjct: 409 NLSVVDACTTRLRLSVVDSGKV-SENELKTIGARGVLKRGATNVQVIIGPEADIIADEIR 467

Query: 544 DLLASG---VDIPEPV------IAESTAGVPTTNFLGKKKDFVAVATGEVIPMAQVNDPV 594
             +  G     + +P        A ST+  P+    G      A A G + P     DP+
Sbjct: 468 TAMERGGNDAGVVKPAASAAAPAAVSTSAAPSATVGGAS----AAANGPLDP-----DPL 518

Query: 595 FSQKMMGDGFAVKPLE 610
               + G    VK L+
Sbjct: 519 RWLAVFGGAGNVKSLD 534



 Score = 34.3 bits (77), Expect = 2e-05
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 7/71 (9%)

Query: 461 SGAAGSGVVDQQIAQIVYLLGGKQNIKEVDA-CMTRLRVSVK-----DREKVGS-EEAWK 513
           + AA +G +D    + + + GG  N+K +DA   TRLR+ V+     DR+++ + + AW 
Sbjct: 505 ASAAANGPLDPDPLRWLAVFGGAGNVKSLDAVAATRLRIVVQDPSAVDRQRLATLDTAWV 564

Query: 514 RAGAMGLIVKD 524
            A  + ++V D
Sbjct: 565 AADTVHIVVGD 575


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: 1089
Number of extensions: 70
Number of successful extensions: 9
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: 599
Length adjustment: 38
Effective length of query: 684
Effective length of database: 561
Effective search space:   383724
Effective search space used:   383724
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:

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