GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagF in Rhodococcus qingshengii djl-6-2

Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate WP_050655247.1 C1M55_RS19650 phosphoenolpyruvate--protein phosphotransferase

Query= TCDB::Q9HXN5
         (842 letters)



>NCBI__GCF_002893965.1:WP_050655247.1
          Length = 557

 Score =  336 bits (862), Expect = 2e-96
 Identities = 222/552 (40%), Positives = 300/552 (54%), Gaps = 25/552 (4%)

Query: 277 AAVAGTLAGVCASPGLASGPLARLGAI--SLPADDGRHRPEEQHLALDQALQRVRDDVQG 334
           A+V   +AG+  S G    P  R      +  AD     PE + + + +AL  V +++  
Sbjct: 3   ASVDNRIAGIGVSAGSVCAPWLRFSTPEPTSAADPITGSPEAELIRIREALDAVAEELLS 62

Query: 335 SLQQARLGGDENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQA 394
             +      +   A I +   A+  D G++ AA   ++ G+  AHA   A  A CE L A
Sbjct: 63  RAKTV----EGVSAEILTTSAAMARDAGIVKAAKANLESGLPTAHAVAVAFDAFCEKLTA 118

Query: 395 LGNLLLAERANDLRDLEKRVLRVLLGDTAPLRVPAGA---IVAAREITPSDLAPLVDAGA 451
           LG  + AERA DLRDL +R + VL G+  P  +PA     I+ AR++ P+D A L  +  
Sbjct: 119 LGGYM-AERATDLRDLGQRAVAVLRGEPMP-GIPAPGYPYILVARDLAPADTATLGTSDV 176

Query: 452 AGLCMAEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRL 511
            GL  AEGG TSH AILA+S G+P +V   +G   L EG+ ++LD   G + + P A   
Sbjct: 177 VGLLTAEGGPTSHTAILAKSLGIPAVVNC-SGTDLLAEGKLLILDGTTGTVTIDPSAEMR 235

Query: 512 EQVALQVAQREEQRRRQQADAQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLR 571
           E+  L+ +   EQ     A AQ    TRDG  + + AN+ +  +AA A A   +GVGL R
Sbjct: 236 ERAVLEASFVAEQ----SASAQGPGRTRDGFAVRLSANIGTLEDAARAGAADCEGVGLFR 291

Query: 572 TEFLFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALG 631
           TEF +L R  AP  EEQ   Y  VL     +KV++RT+D G DK L +L L VEENPALG
Sbjct: 292 TEFSYLGRHDAPSVEEQAQTYASVLGHFAGQKVVVRTLDSGSDKPLPFLDLGVEENPALG 351

Query: 632 LRGIHLGQARPELLDQQLRALLRVEPLERCR--ILLPMVSEVDELRAIRRRLGELATQLG 689
           +RG+ +G   P+ L  QL AL            ++ PMV+  DE +       ELA   G
Sbjct: 352 IRGLRVGTVYPDTLISQLDALAAAGNATGADLWVMAPMVATADEAKDF----AELARSRG 407

Query: 690 IERLPELGVMIEVPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHP 749
           I ++   G MIEVP+AAL A  + EH DF+SIGTNDLSQY  A+DR   GLA  +D   P
Sbjct: 408 IGKV---GAMIEVPAAALRAKDILEHLDFVSIGTNDLSQYTCAVDRMAGGLAQLLDPWQP 464

Query: 750 ALLRLIAQTCAGAARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQ 809
           A+L LIA      A  G+ VGVCG  ASDPL  PVLVGLGV  LS+    +G ++ ++  
Sbjct: 465 AVLDLIAMVGQAGADAGKPVGVCGESASDPLLAPVLVGLGVTSLSMSVPALGAVRAQLAS 524

Query: 810 LDAAECRRHAQA 821
           LD A C+  A A
Sbjct: 525 LDLAVCKDMAAA 536


Lambda     K      H
   0.319    0.136    0.390 

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: 1067
Number of extensions: 51
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: 842
Length of database: 557
Length adjustment: 39
Effective length of query: 803
Effective length of database: 518
Effective search space:   415954
Effective search space used:   415954
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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