GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Marinobacter algicola DG893

Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate WP_007154627.1 MDG893_RS14835 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::pseudo3_N2E3:AO353_05485
         (953 letters)



>NCBI__GCF_000170835.1:WP_007154627.1
          Length = 768

 Score =  330 bits (845), Expect = 3e-94
 Identities = 211/593 (35%), Positives = 325/593 (54%), Gaps = 20/593 (3%)

Query: 376 LPTVSAQSEVIDEITDVVVA--PASGCVIQAVAAAPGIAIGPAHIQVLQAIDYPLRGEST 433
           L  V A SE    I+ + +    A+      V  APG+AIG   + V  A D  +  E  
Sbjct: 151 LAGVIAHSEATGAISGLSLTGEEATDVSFSGVPGAPGVAIGKG-VVVYPAADLDVVPEKP 209

Query: 434 AIERERLKTSLAD-----VRRDIEGLIQRSKAKAIRE---IFITHQEMLDDPELTDEVDT 485
             + E L+ SL D     VR DIE +  R  ++   E   +F  +  ML D  +  EV  
Sbjct: 210 TDDVE-LELSLFDGAVTAVREDIERVAARLASQLRPEEQALFDVYLRMLGDDAMPGEVGN 268

Query: 486 RLKQGESAEAAWMAVIDAAARQQESLQDALLAERAADLRDIGRRVLAQLC-GIETPSEPD 544
           R+K+G  A+ A   V+    R  E + D  L ERA D+RD+GRR+L+ L  G +  +   
Sbjct: 269 RIKEGFWAQGALKQVVQQYVRHFEMMDDHYLQERAVDIRDLGRRLLSHLQEGEQKDTVYP 328

Query: 545 QPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAVLRLA 604
           +  +LV +E+ P+ +  +   ++ G+++ +G + +H AI+ARA+G+P ++G     +   
Sbjct: 329 ENTVLVSEELTPAMLGEVPKGQLVGLVSVKGSSNSHVAILARAMGVPTVMGLVDIPVNQL 388

Query: 605 SGTPLLLDGQRGRLHVDADAATLQRAAEERDNREQRLQAAAAQRHQPALTTDGHAVEVFA 664
            G  L++DG  G++             E  D  ++ ++   A R  P  TTD H V +  
Sbjct: 389 DGKDLIVDGFEGQIFASPSTDLRNFYQEICDEEDELVKGLEALRDLPCETTDNHRVSLLV 448

Query: 665 NIGESAGVVSAVEQGAEGIGLLRTELIFMAHQQAPDEATQEVEYRRVLDGLAGRPLVVRT 724
           N G    VV ++  GAEGIGL RTE+ FM   + P E  Q   YR  L+  A  P+ +RT
Sbjct: 449 NTGLMTDVVRSLSHGAEGIGLYRTEVPFMIKDRFPSEQEQREYYREQLEAFAPNPVTMRT 508

Query: 725 LDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAADN-RPLRIMFPM 783
           LD+GGDK L Y+PI +EENPFLG RGIR+TL  P+I   Q+RA+L+A++    L+IM PM
Sbjct: 509 LDIGGDKALTYFPI-QEENPFLGWRGIRVTLDHPEIFLVQVRAMLKASEGLNNLQIMLPM 567

Query: 784 VGSVDEWRQARDMTERLRLEI-----PVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGT 838
           + ++ E  ++  +  R+  E+      +   ++G+M+E+P+A      LA  VDF SVG+
Sbjct: 568 ISNISEVEESLHLIYRVYHEVREEGYNIHMPKVGVMVEIPAAVYQIRELADRVDFLSVGS 627

Query: 839 NDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVP 898
           NDLTQY LA+DR +P ++      HPAVLQ +    + AHA GK VG+CGELA DP    
Sbjct: 628 NDLTQYLLAVDRNNPRVAQLYHSYHPAVLQALVRVAQDAHAVGKPVGICGELAGDPGGAL 687

Query: 899 VLVGLGVDELSVSARSIGEVKARVRELSLAQVKHLAQLALAVGSANEVRALVE 951
           +L+ +G D LS++A S+ +VK+ +R +S      L +  L + S + +++ V+
Sbjct: 688 LLMAMGYDSLSMNAASLPKVKSVIRSVSREWSAQLLEDVLLLDSPHVIKSCVD 740


Lambda     K      H
   0.319    0.135    0.383 

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: 1355
Number of extensions: 58
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: 953
Length of database: 768
Length adjustment: 42
Effective length of query: 911
Effective length of database: 726
Effective search space:   661386
Effective search space used:   661386
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: 56 (26.2 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