GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__MR1:200788
          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.

Links

Downloads

Related tools

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