GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Herbaspirillum seropedicae SmR1

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate HSERO_RS11260 HSERO_RS11260 aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__HerbieS:HSERO_RS11260
          Length = 477

 Score =  317 bits (812), Expect = 6e-91
 Identities = 192/475 (40%), Positives = 265/475 (55%), Gaps = 11/475 (2%)

Query: 23  FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82
           FI   + A    E+   +DP    P   IARG + DID+A+ AAR  +E G W   S A+
Sbjct: 5   FIANRWVAPTSGESIPVLDPSDGQPFDAIARGNATDIDQAVRAARLAYE-GAWGRLSAAE 63

Query: 83  RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142
           R  +L KLA  ++ H EELA LE  D GKP++ + R D     R   +YA A DK++G+ 
Sbjct: 64  RSRLLMKLAYKLQDHQEELAQLEGRDCGKPMKQA-RADAAAIVRYFEFYAGAADKLHGDT 122

Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202
               +    + +REP GV   IVPWN+P+ +    +G ALAAGN+ ++KP+E + LS +R
Sbjct: 123 IPYQAGYTVLTLREPHGVTGHIVPWNYPMQIFGRCVGGALAAGNTCVVKPAEDACLSILR 182

Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262
           +A LA E G P+G LN+VTG+GHEAG  L +H D++ I+FTGS   GK +++ A + +  
Sbjct: 183 VAELAAEVGFPEGALNIVTGYGHEAGDLLVKHPDVNHISFTGSPNVGKLVVRAAAEHHTP 242

Query: 263 RVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALL 322
            V LE GGKS  IVF D  D++         I  N GQ C AG+RLL++    ++ L  L
Sbjct: 243 -VTLELGGKSPQIVFEDA-DMEAMLPVVVNAIVQNAGQTCSAGSRLLVQRGAYEQVLERL 300

Query: 323 KQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG-QLLLDGRNAGLAAAIG- 380
                  Q G         G LI     + V  F+ + +  G  L   G+ A      G 
Sbjct: 301 SGLFSQLQVGSS-QMDLDCGPLIRKTQQERVAGFLSDAQRDGIALAAQGKIAAGVPTGGF 359

Query: 381 ---PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRA 437
              P +  DV P   L++EE+FGPVL    F  E  A+ LAN + YGL A+VWTRD  R 
Sbjct: 360 YQAPALLRDVPPRHRLAQEEVFGPVLAAMPFEDEAHAIALANGTDYGLVASVWTRDGGRQ 419

Query: 438 HRMSRRLKAGSVFVNNYN-DGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491
            R++R +++G VF+NNY   G + +PFGG K SG+GR+K   AL  FT LKTI I
Sbjct: 420 MRLARAIRSGQVFINNYGAGGGVELPFGGVKASGHGREKGFEALYGFTVLKTIAI 474


Lambda     K      H
   0.317    0.133    0.389 

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: 563
Number of extensions: 30
Number of successful extensions: 7
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: 495
Length of database: 477
Length adjustment: 34
Effective length of query: 461
Effective length of database: 443
Effective search space:   204223
Effective search space used:   204223
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.

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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:

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