GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gamP 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)



>lcl|FitnessBrowser__MR1:200788 SO1623 PTS system, glucose-specific
           IIBC component (NCBI ptt file)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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