GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Herbaspirillum seropedicae SmR1

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate HSERO_RS13690 HSERO_RS13690 diaminopimelate decarboxylase

Query= curated2:Q9PII5
         (402 letters)



>FitnessBrowser__HerbieS:HSERO_RS13690
          Length = 418

 Score =  146 bits (369), Expect = 1e-39
 Identities = 110/367 (29%), Positives = 184/367 (50%), Gaps = 21/367 (5%)

Query: 12  TPFYIYNFDFIKERFLNLKEAFKARKSQIFYAVKANSNLSLLQMLANLDSGFDCVSIGEV 71
           TPFY+Y+   ++ R  +L+    A  + + Y++KAN   +L+Q +A L  GFD  S GE+
Sbjct: 41  TPFYVYDRALLRARVAHLRAHLPAELA-LHYSIKANPMPALVQAMAQLVDGFDVASGGEL 99

Query: 72  KRALKAGAKAYKIIFSGVGKTKEELRQALEYDILYINLESEAEMMLLESVAKELNLKARI 131
             AL        I F+G GK+  ELR+AL   ++ +++ESE E   + ++A+EL ++  +
Sbjct: 100 ATALDTPMPVQHISFTGPGKSLAELRRALAAGVM-LHVESEREAEAVAALAQELGVRPGV 158

Query: 132 SIRVNPNVDAKTHPYISTGLNENKFGVEIDIARKMYLYAKNSSFLEPVGVHFHIGSQLLD 191
           ++R+NP  + K+   +  G     FGV+ + A  +  +      ++  G+    GSQ LD
Sbjct: 159 TLRINPPFELKSSG-MRMGGGAKPFGVDAEAAPALLRWLAGQG-VQVAGLQIFCGSQSLD 216

Query: 192 ISPIHEAAAIVAKLVRELKA-LQIDLKFFDIGGGLGVAYEKNECEPDLYDYAQGI---LA 247
              I  A +   +L  +L     + L+  +IGGG G+ Y   E   ++      +   L 
Sbjct: 217 AQAIMAAQSSSFELALQLAGEAGLSLRVLNIGGGFGIPYFPGERALEIAPIGAHLAQWLP 276

Query: 248 QLHGL--DLTIGMEPGRYLVAKSGEFVCSVLYEKQNKTKRFVVVDGAMNDLIRPS----- 300
           +L  L   L + ME GRYLV ++G +V  V+  KQ++ + F+VVDG ++  +  S     
Sbjct: 277 RLRALHPQLRVVMEMGRYLVGEAGLYVSRVIDRKQSRGEVFLVVDGGLHHHLAASGNFGQ 336

Query: 301 -LYEAYHEIILPYNQ-----GEESLCDVVGGICESGDFFAKARSLPSTQSDDIMVIKNTG 354
            + + Y   I+P        G      VVG +C   D  A    LP+    D++V+  +G
Sbjct: 337 VIRKNYPVTIVPQQPQRSGGGTTERVSVVGPLCTPLDVLAAQMLLPAAAVGDLVVVFQSG 396

Query: 355 AYGFSMS 361
           AYG S S
Sbjct: 397 AYGLSAS 403


Lambda     K      H
   0.319    0.137    0.385 

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: 326
Number of extensions: 19
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: 402
Length of database: 418
Length adjustment: 31
Effective length of query: 371
Effective length of database: 387
Effective search space:   143577
Effective search space used:   143577
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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