GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS02745
          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:

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