GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagF in Thauera aminoaromatica S2

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_004265629.1 C665_RS00525 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::pseudo5_N2C3_1:AO356_17540
         (837 letters)



>NCBI__GCF_000310185.1:WP_004265629.1
          Length = 576

 Score =  317 bits (811), Expect = 2e-90
 Identities = 202/569 (35%), Positives = 303/569 (53%), Gaps = 14/569 (2%)

Query: 278 LHGVCAAPGLVTGPLVRLSGIQLPED---IGGHAIEEQRQRLSDALAQVRGE-IHLTLEH 333
           LHG+  + G+  G +  +S   L  +   +    ++++  RL +ALA V+GE I L    
Sbjct: 5   LHGLAVSQGIAIGHVHLVSHALLEVNHYHVAPRYLDDELARLDEALATVQGELIGLKAIT 64

Query: 334 ARARQHRDEEAIFSAHLALLEDPVLLDAA-DLFIEQGSAAPHAWSRSIDTQCQVLQQLGS 392
              + H +  A     L +L DP+L+DAA  L  E+   A  A  + ++   +  +Q+  
Sbjct: 65  TSGQAHSEVGAFVDLQLMMLADPMLVDAARQLVTERRCNAEWALVQQMEHLVEQFRQIED 124

Query: 393 TLLAERANDLRDLRQRVLRVLLGEAWQFDV----AAGAIVAAQELTPSDLLQLSAQGVAG 448
             L ER  D+  + +R+++VLLG             G+IV A +L+P+D +      +AG
Sbjct: 125 PYLRERQADVVQVVERLVKVLLGHPGHLPPRRRDGLGSIVVAHDLSPADTIGFRDHNIAG 184

Query: 449 VCMVEGGATSHVAILARGKGLPCLVALGDELLAQEQGQAVVLDADGGRLELTPTVERLAQ 508
                GG TSH AI+AR   +P +V L       E  + +++D   G + + P  + + +
Sbjct: 185 FVTDVGGPTSHTAIVARSLKIPAVVGLHHVRDLLEDDELIIVDGTRGVIIVAPDEQIVEE 244

Query: 509 VRQAQTRRTALRAQQQSLAHTPARTVDGVEVEVAANVASSAEAGESLANGADGVGLLRTE 568
            R  ++     R++   L  T A T+DG EV + AN+    +     +  ADG+GL RTE
Sbjct: 245 YRLRRSELEIERSKLNRLRDTRAATLDGEEVNLLANIEGPKDLPAVKSANADGIGLYRTE 304

Query: 569 FLFVDRHTAPDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGDKQLDYLPLPSEANPVLGLR 628
           FLF+ R T PDEEEQ +AY+AV++A+  KPV IRT DVG DK L+      E NP LGLR
Sbjct: 305 FLFIGRDTLPDEEEQYEAYRAVVKALPGKPVTIRTFDVGADKALNGAQAREEPNPALGLR 364

Query: 629 GIRLAQVRPDLLDQQLRALLQTRPLDRCRILLPMVT---EVDELLHI--RKRLDALGSEL 683
            +R +   P +   QLRALL+     R +I++PM+    EVD+ L +  + + +    ++
Sbjct: 365 AVRYSLAEPKMFKTQLRALLRASAHGRLQIMVPMLAHAQEVDQCLTLLEKAKAELRAEKI 424

Query: 684 GLSERPQLGVMVEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALH 743
              E  ++G M+EVPAAAL          FLSIGTNDL QYTLA+DR    +A   D LH
Sbjct: 425 KFDEGIRIGGMIEVPAAALSLGMFIRRLAFLSIGTNDLIQYTLAIDRSDEAVAHLYDPLH 484

Query: 744 PALLRLIAQTCAGAAKHGRWVGVCGALASDPLATPVLIGLGVRELSVSPPQIGEIKDRVR 803
           PA+L+LIA T +  A+ G  V VCG +A DPL T +L+G+G+R  S+ P  I EIK +V 
Sbjct: 485 PAVLKLIAGTISSGARFGLPVSVCGEMAGDPLYTELLLGMGLRNFSMHPGSILEIKQQVL 544

Query: 804 HLDAAQCARLSNELLNLGSALAVRRACHR 832
             D  + A     +L +     +R A  R
Sbjct: 545 RADLGELAPRVQRILKMDEPARIREAVER 573


Lambda     K      H
   0.319    0.134    0.386 

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: 970
Number of extensions: 44
Number of successful extensions: 4
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: 837
Length of database: 576
Length adjustment: 39
Effective length of query: 798
Effective length of database: 537
Effective search space:   428526
Effective search space used:   428526
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 (21.8 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. 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