GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagEIIA in Burkholderia phytofirmans PsJN

Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate BPHYT_RS02745 BPHYT_RS02745 PTS system N-acetylglucosamine-specific transporter subunit IIBC

Query= SwissProt::P39816
         (631 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS02745 BPHYT_RS02745 PTS system
           N-acetylglucosamine-specific transporter subunit IIBC
          Length = 591

 Score =  434 bits (1117), Expect = e-126
 Identities = 237/503 (47%), Positives = 318/503 (63%), Gaps = 31/503 (6%)

Query: 6   FQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAVGVAIG 65
           F  +Q+LGRALM P+AVLP AGLLLR G  D+ NI +I DAGG +FDNLPL+FA+GVA+G
Sbjct: 6   FLKIQRLGRALMLPIAVLPVAGLLLRLGQPDVFNIKMIADAGGAIFDNLPLLFAIGVAVG 65

Query: 66  LA-GGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIGLLAAY 124
            A    GVAGLA  IGYLI    + ++   L             +MGV  GI+ G++A  
Sbjct: 66  FAKDNNGVAGLAGAIGYLIEVAVMKDINDKL-------------NMGVLSGIVAGIVAGL 112

Query: 125 LYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASS-LIADS 183
           LY R+  I+L   L FF GKRFVPI+T V  LV+G+ F +VW  +Q  I+ A   L    
Sbjct: 113 LYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAGHWLTTAG 172

Query: 184 TVGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDPTAGRF 243
            +G F +  + RLL+  GLHHI  +  +F+ G +T P  G  VTGDL RFFAGDPTAG F
Sbjct: 173 ALGAFVFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPG-GAAVTGDLHRFFAGDPTAGTF 231

Query: 244 MMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITEPVEFSFLFVAP 303
           M G FP M+F LPA  LA+ H A  E++ ++ G++ S ALTS LTG+TEP+EFSF+F+AP
Sbjct: 232 MTGFFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAP 291

Query: 304 VLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGLSTNGWVVIPVGIVFAFIYY 363
           VLY+I+++L G+   +C    +  G+TFS G IDYVLNYGLST GW  IP+G+V+  +YY
Sbjct: 292 VLYVIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPIGLVYMVVYY 351

Query: 364 YLFRFAILKWNLKTPGRE-------TDEDGQNEEKAPVAKDQL--AFHVLQALGGQQNIA 414
            LFRF I K+N+ TPGRE        D        +PVA   +  A   + ALGG  N++
Sbjct: 352 GLFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASNLS 411

Query: 415 NLDACITRLRVTVHQPSQVCKDELKRLGAVGVLE-VNNNFQAIFGTKSDALKDDIKTIMA 473
            +DAC TRLR++V   ++V ++ELK +GA GVL+  + N Q I G ++D + D+I+T++A
Sbjct: 412 VVDACTTRLRLSVVDSNKVSENELKTIGARGVLKRGSTNVQVIIGPEADIIADEIRTVIA 471

Query: 474 GG-----VPATAAALDTVTDKPL 491
            G      PA AA    V   P+
Sbjct: 472 QGGGDAVKPAAAAPAQVVAAAPV 494



 Score = 32.0 bits (71), Expect = 8e-05
 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 7/86 (8%)

Query: 393 PVAKDQLAFHVLQALGGQQNIANLDA-CITRLRVTVHQPSQVCKDELKRLGAVGVLEVNN 451
           P+  D L +  L   GG  N+ +LDA   TRLR+ V  PS V +  L  L    +    +
Sbjct: 504 PLDPDPLRW--LAVFGGAGNVLSLDAIAATRLRIVVRDPSAVDRQRLATLDTAWISA--D 559

Query: 452 NFQAIFGTKSDALKDDI--KTIMAGG 475
            F  + G  +    + +  +T  +GG
Sbjct: 560 TFHIVVGDAAQRYAEKLATRTTQSGG 585


Lambda     K      H
   0.324    0.142    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: 1000
Number of extensions: 49
Number of successful extensions: 6
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: 631
Length of database: 591
Length adjustment: 37
Effective length of query: 594
Effective length of database: 554
Effective search space:   329076
Effective search space used:   329076
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: 41 (22.0 bits)
S2: 53 (25.0 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