GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_02007
          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 (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