GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Rhizobium etli CFN 42

Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_011428504.1 RHE_RS27450 aldehyde dehydrogenase

Query= metacyc::MONOMER-13361
         (500 letters)



>NCBI__GCF_000092045.1:WP_011428504.1
          Length = 504

 Score =  333 bits (853), Expect = 1e-95
 Identities = 186/479 (38%), Positives = 267/479 (55%), Gaps = 8/479 (1%)

Query: 23  YIDGNFVT--SASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGP-WGKLSVQD 79
           +I+G FV   + +  A+ +P  G+   D+  ADA  V  AV AA  A + P W +++  D
Sbjct: 16  FINGEFVAPKAGNYIASYDPTTGERWYDLAAADANDVAAAVAAANAAFRNPAWRRMTQTD 75

Query: 80  RAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDL 139
           R AL+ K+A+ ++A  +     E  D G+ + + R   +     ++  FA +A     D 
Sbjct: 76  RGALVRKLAELVRANADTLAEIETRDNGKLLKETRA-QMRSMPDSYHYFAGMADKLQGDT 134

Query: 140 FEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPS 199
             ++  D    LN  +R+PLGV+G+I+PWN PL+L T  +AP LA GNTVV KPSE + +
Sbjct: 135 IPINRMD---TLNINLREPLGVVGMITPWNSPLMLLTGTLAPCLAIGNTVVIKPSEHATA 191

Query: 200 SATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVA 259
           S   LAE++H+AG P GV N++ G GK SAGE LT+HPG++   FTG + TG  I    A
Sbjct: 192 STLALAELIHEAGFPAGVVNVVTGTGK-SAGEALTRHPGVAKYVFTGSTATGRRIAGNAA 250

Query: 260 DGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFV 319
             +   S ELGGK+  VVF D +L+ A+ GV+   F  +GQ C+   R +V  SI+D+F+
Sbjct: 251 QNLVPCSMELGGKSPHVVFGDVELEHAVNGVVSGVFAAAGQTCVAGSRCFVEASIYDKFI 310

Query: 320 SGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDE 379
             L     R+ VG P  D  ++GPL       KV  Y    V +GA +  GG  P+  D 
Sbjct: 311 DALIARTARIRVGLPTLDDTDIGPLALADQLSKVEGYVASGVKDGAKIAAGGRRPRKEDL 370

Query: 380 RDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTT 439
            + G Y +PT+     +    + +EIFGPV  + PF DE E++   NDS+YGLA  IWT 
Sbjct: 371 SNGGWYYEPTVMVDAQNDMGFMRDEIFGPVVGVMPFRDEAEMVALANDSHYGLASGIWTK 430

Query: 440 NLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICI 498
           ++ RA R + QI  G VWVNT+      +  GG K SG GR GG   M  +S + N+ I
Sbjct: 431 DIDRALRFANQIEAGTVWVNTYRSASFMSANGGFKESGYGRRGGFEVMHEFSRLKNVII 489


Lambda     K      H
   0.318    0.135    0.405 

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: 585
Number of extensions: 23
Number of successful extensions: 3
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: 500
Length of database: 504
Length adjustment: 34
Effective length of query: 466
Effective length of database: 470
Effective search space:   219020
Effective search space used:   219020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 Apr 09 2024. 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