GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Sinorhizobium meliloti 1021

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate SMa2213 SMa2213 aldehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>FitnessBrowser__Smeli:SMa2213
          Length = 494

 Score =  357 bits (917), Expect = e-103
 Identities = 194/462 (41%), Positives = 278/462 (60%), Gaps = 9/462 (1%)

Query: 14  FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALN-GPWKKMTANE 72
           +IDG++V    G+  + ++P T      V  G A + D AV+AA +A + GPW KM   E
Sbjct: 10  YIDGQWVAPASGEYIETVDPFTARPWALVPRGNAEDADRAVRAAHRAFSQGPWGKMHPTE 69

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKP-TWLSGSID-IPRAAYNFHFFSDYIRTITN 130
           R  ++++   LI E  + L+ +E  D G+    ++  I  IPR    +H+++ +   I  
Sbjct: 70  RGRIIQRFAALIEEHADALADIEVRDNGRLLAEMTHQIRYIPRW---YHYYAGFADKIEG 126

Query: 131 EATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTA 190
                D  AL+++   P+GV   I PWN PLLL + K APALAAGNT+VMKPAE T  TA
Sbjct: 127 TLHPCDKPALSFSRHEPLGVCVGIVPWNAPLLLFSLKAAPALAAGNTLVMKPAEFTSATA 186

Query: 191 TVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKT 250
             L E+   AG P GV+N+V G+GP   G  L  HP    + FTG T TG  + + AAK 
Sbjct: 187 LKLMELVEKAGFPTGVINVVTGYGPE-VGEPLVTHPLTRHVGFTGSTKTGAHLYSLAAKD 245

Query: 251 LKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEK 310
           +KR+S ELGGK+PN++F D++LD  +   +   F   G+ C+ GSR+ V R  ++ FLEK
Sbjct: 246 VKRVSLELGGKSPNIVFGDADLDNAVRGVVGGIFGAVGQTCIAGSRLLVHRSIHDEFLEK 305

Query: 311 FVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRP--EGLEK 368
               TK   +GDP   +T++G + +   +E+V GYI +A  EG  ++ GG RP  E    
Sbjct: 306 LAVFTKTARIGDPRKVETQIGPIANSMQFEKVLGYIDIARREGAELILGGGRPDLEECGT 365

Query: 369 GYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLR 428
           GYF+EPTI  G++ D R+ +EE+FGPV++ I FD  EE L   ND+ +GL A VWT+D+R
Sbjct: 366 GYFIEPTIFAGVSNDMRIAREEVFGPVLSAIVFDEPEEALAIANDSEFGLGAGVWTSDMR 425

Query: 429 RAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGL 470
            A +++ ++EAG VWVNT+      TPFGG K+SGIGRE G+
Sbjct: 426 LALKMSERLEAGSVWVNTYRDISYTTPFGGYKKSGIGRENGV 467


Lambda     K      H
   0.318    0.136    0.404 

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: 624
Number of extensions: 24
Number of successful extensions: 5
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: 486
Length of database: 494
Length adjustment: 34
Effective length of query: 452
Effective length of database: 460
Effective search space:   207920
Effective search space used:   207920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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