GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagEcb in Shewanella oneidensis MR-1

Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)

Query= reanno::BFirm:BPHYT_RS02745
         (591 letters)



>lcl|FitnessBrowser__MR1:200788 SO1623 PTS system, glucose-specific
           IIBC component (NCBI ptt file)
          Length = 499

 Score =  274 bits (700), Expect = 7e-78
 Identities = 169/473 (35%), Positives = 253/473 (53%), Gaps = 40/473 (8%)

Query: 10  QRLGRALMLPIAVLPVAGLLLRLG------QPDVFNIKMIADAGGAIFDNLPLLFAIGVA 63
           QRL +AL++PIA+LP AG++L L        P+V N+ M+A  G  IF  +P+LFA+ VA
Sbjct: 29  QRLSQALLIPIAILPAAGVMLGLTVSPIPFMPEVLNVLMLA-VGKLIFAIMPILFAVAVA 87

Query: 64  VGFAKDNNGVAGLAGAIGYLIEVAVMKDIND-------------KLNMGVLSGIVAGIVA 110
           +GF +D  G+A      GY +  A +  + D              L+ G+  G++ G V 
Sbjct: 88  IGFCRDQ-GIAAFTAVFGYGVMTATLAALADLYQLPTQLVLGMETLDTGIAGGMLIGGVT 146

Query: 111 GLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAGHWLTT 170
                  + I+LP   +FF G+R   ++   + + LG    ++W  +  +I+    W   
Sbjct: 147 CFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYVLAHIWPSLSLLIERVSDWAVY 206

Query: 171 AGALGAF-VFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFFAGDPTAG 229
                AF V+G L RLL+  GLHHI N+  +   G +       V G++ R+ AGDP AG
Sbjct: 207 QKPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQYQLQDAEVVRGEVARYLAGDPQAG 266

Query: 230 TFMTGFFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFL 289
               G+  + M+GLPAA LA++  A    R  V G++ S A  S+LTGVTEPIEF+FMF+
Sbjct: 267 NLAGGYL-IKMWGLPAAALAIWRCADNSERNRVAGIMLSAAAASWLTGVTEPIEFAFMFV 325

Query: 290 APVLYVIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPIGLVYMVV 349
           AP+L++IH +L+G++  +C  L IH    FS G +D+ L + LS    W   +G +  V+
Sbjct: 326 APLLFLIHVMLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFAVLGPLTAVI 385

Query: 350 YYGLFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASN 409
           YY LFR  I  FN+ TPGR        + S    G        +    +  IAALGG  N
Sbjct: 386 YYILFRGSILAFNLKTPGR--------LQSDGTKG--------SKESLRAIIAALGGRDN 429

Query: 410 LSVVDACTTRLRLSVVDSNKVSENELKTIGARGVLKRGSTNVQVIIGPEADII 462
           +  ++AC TRLRLSV     V++  L  +GA+GV+  G   VQ++ G +A+ +
Sbjct: 430 IVELNACLTRLRLSVHSPELVNKVRLSQLGAKGVIVMGK-GVQIVYGTKAETL 481


Lambda     K      H
   0.325    0.141    0.426 

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: 833
Number of extensions: 44
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: 591
Length of database: 499
Length adjustment: 35
Effective length of query: 556
Effective length of database: 464
Effective search space:   257984
Effective search space used:   257984
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: 40 (21.6 bits)
S2: 52 (24.6 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