GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEIIA in Shewanella oneidensis MR-1

Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)

Query= SwissProt::P39816
         (631 letters)



>FitnessBrowser__MR1:200788
          Length = 499

 Score =  307 bits (787), Expect = 6e-88
 Identities = 173/468 (36%), Positives = 268/468 (57%), Gaps = 18/468 (3%)

Query: 6   FQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDA-----GGVVFDNLPLIFAV 60
           F+  Q+L +AL+ P+A+LPAAG++L      +  +P + +      G ++F  +P++FAV
Sbjct: 25  FKFAQRLSQALLIPIAILPAAGVMLGLTVSPIPFMPEVLNVLMLAVGKLIFAIMPILFAV 84

Query: 61  GVAIGLAGGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIGL 120
            VAIG    +G+A   AV GY ++T TL  +  L  L          +D G+ GG++IG 
Sbjct: 85  AVAIGFCRDQGIAAFTAVFGYGVMTATLAALADLYQLPTQLVLGMETLDTGIAGGMLIGG 144

Query: 121 LAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASSLI 180
           +  +  +    I L  +  FF G+R   ++    ++ +G + + +WP +   I   S   
Sbjct: 145 VTCFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYVLAHIWPSLSLLIERVSDWA 204

Query: 181 ADSTVGLFF--YATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDP 238
                 + F  Y  + RLLIP GLHHI+  PFY  +G+Y        V G++ R+ AGDP
Sbjct: 205 VYQKPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQY-QLQDAEVVRGEVARYLAGDP 263

Query: 239 TAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITEPVEFSF 298
            AG  + G +   ++ LPA ALAI   A   ++  ++G+M+SAA  S LTG+TEP+EF+F
Sbjct: 264 QAGN-LAGGYLIKMWGLPAAALAIWRCADNSERNRVAGIMLSAAAASWLTGVTEPIEFAF 322

Query: 299 LFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGLSTN-GWVVIPVGIV 357
           +FVAP+L+LI+ +L+G+ + VC +  + H   FS G +D+ L + LS N GW  + +G +
Sbjct: 323 MFVAPLLFLIHVMLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFAV-LGPL 381

Query: 358 FAFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLD 417
            A IYY LFR +IL +NLKTPGR    DG    K  +        ++ ALGG+ NI  L+
Sbjct: 382 TAVIYYILFRGSILAFNLKTPGR-LQSDGTKGSKESLRA------IIAALGGRDNIVELN 434

Query: 418 ACITRLRVTVHQPSQVCKDELKRLGAVGVLEVNNNFQAIFGTKSDALK 465
           AC+TRLR++VH P  V K  L +LGA GV+ +    Q ++GTK++ L+
Sbjct: 435 ACLTRLRLSVHSPELVNKVRLSQLGAKGVIVMGKGVQIVYGTKAETLR 482


Lambda     K      H
   0.324    0.142    0.421 

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: 712
Number of extensions: 36
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: 631
Length of database: 499
Length adjustment: 36
Effective length of query: 595
Effective length of database: 463
Effective search space:   275485
Effective search space used:   275485
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 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