GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagF in Paraburkholderia bryophila 376MFSha3.1

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate H281DRAFT_02007 H281DRAFT_02007 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::BFirm:BPHYT_RS02740
         (854 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02007 H281DRAFT_02007
           phosphoenolpyruvate--protein phosphotransferase
          Length = 582

 Score =  276 bits (707), Expect = 2e-78
 Identities = 197/573 (34%), Positives = 288/573 (50%), Gaps = 19/573 (3%)

Query: 292 TLAGVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRL--LDKAIATVDADLDTTVRD 349
           TL G+  + G+A+G+      A +D        +  ES +     A   V  +LD    D
Sbjct: 4   TLHGIPVSRGIAIGRAYLIAPAALDVDHYLIEPAQIESEVERFRAAQQRVHEELDALRAD 63

Query: 350 ASQRGAVGEAGIF-SVHRVLLEDPTLLDAARDLISLGK-SAGFAWREAIRAQIAILTNIE 407
            +   A  E G F +VH ++L D  L+    DLI   + +  +A  E +        +IE
Sbjct: 64  LAA-DAPSEMGAFINVHSMILNDAMLVQETIDLIRTRRYNVEWALTEQLERLSRHFDDIE 122

Query: 408 DALLAERAADLRDIEKRVLRALGYTSAT----ARTLPEEAVLAAEEFTPSDLSTLDRSRV 463
           D  L ER AD+  + +RVL+AL   S +         +E ++ A +  P+D+        
Sbjct: 123 DEYLRERKADIEQVVERVLKALAGASGSLVNGVHGACDEMIVVAHDIAPADMMQFKTQTF 182

Query: 464 TALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDV 523
              V   GG TSH AI+AR  GIPA V V  A   I +   ++V+   G +   P  + +
Sbjct: 183 QGFVTDLGGRTSHTAIVARSLGIPAAVGVQHASALIRQDDLIIVDGDHGIVIVDPAPIVL 242

Query: 524 ERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLR 583
           E     ++  A  +   +R       T  G  IE+ ANI   +DA+ AV+ GA  VGL R
Sbjct: 243 EEYSYRQSEKALEQRKLQRLKFSPTQTLCGTRIELCANIELPEDARAAVDAGATGVGLFR 302

Query: 584 TELLFI-HRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLT----LPPEP 638
           TE LF+ H+   P  +E  ++Y+  V+ ++G    IRT+DVGADK +D ++         
Sbjct: 303 TEFLFMNHKHRMPEEEEQFEAYRRAVELMNGLPVTIRTIDVGADKPLDSMSGGDGYETAA 362

Query: 639 NPALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFAR 698
           NPALGLR IR +   P +   QLR +L     G V+IL+PM+    E+ +    I E  R
Sbjct: 363 NPALGLRAIRWSLSEPQMFLTQLRAILRASAFGTVKILVPMLAHAQEIDQTLDLIREAKR 422

Query: 699 ELGRT----EP-IEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLA 753
           +L       +P ++VG MIE+P+AA+      +  DFLSIGTNDL QYTLA+DR    +A
Sbjct: 423 QLDDAGIAYDPNVQVGAMIEIPAAAIALPLFLKRLDFLSIGTNDLIQYTLAIDRADNSVA 482

Query: 754 AQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVP 813
              D LHPAVL LIA T++ A + G  V VCG +AGDP    LL+G+G+TE S+ P  + 
Sbjct: 483 HLYDPLHPAVLHLIAFTLREAKRAGVPVSVCGEMAGDPSLTRLLLGMGLTEFSMHPSQLL 542

Query: 814 GIKARVRNLDYQLCRQRAQDALALESAQAVRAA 846
            +K  V     +   +   D LA    + V+AA
Sbjct: 543 VVKQEVLRSHLKTLEKPVADVLASFEPEEVQAA 575


Lambda     K      H
   0.317    0.133    0.371 

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: 1017
Number of extensions: 52
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: 854
Length of database: 582
Length adjustment: 39
Effective length of query: 815
Effective length of database: 543
Effective search space:   442545
Effective search space used:   442545
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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