GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cyclodeaminase in Rhizorhabdus wittichii RW1

Align Ornithine cyclodeaminase; OCD; EC 4.3.1.12 (characterized)
to candidate WP_011951896.1 SWIT_RS05355 ornithine cyclodeaminase

Query= SwissProt::P09773
         (354 letters)



>NCBI__GCF_000016765.1:WP_011951896.1
          Length = 346

 Score =  497 bits (1280), Expect = e-145
 Identities = 239/343 (69%), Positives = 286/343 (83%)

Query: 7   LNIVPFISVENMMDLAVSTGIENFLVQLAGYIEEDFRRWESFDKIPRIASHSRDGVIELM 66
           LN VPF+SV++MM + +  G+E  LV+LA Y+E+DFRRW+ FDK PR+ASHSR+GVIELM
Sbjct: 3   LNTVPFVSVDHMMRIVLDIGVERVLVELADYVEDDFRRWDCFDKTPRVASHSREGVIELM 62

Query: 67  PTSDGTLYGFKYVNGHPKNTKSGRQTVTAFGVLSDVDSGYPLLLSEMTILTALRTAATSA 126
           PTSDG +YGFKYVNGHP N + G QTVTAFGVL+ VDSGYPL+LSEMT+LTALRTAATSA
Sbjct: 63  PTSDGEVYGFKYVNGHPSNMQRGLQTVTAFGVLAAVDSGYPLMLSEMTLLTALRTAATSA 122

Query: 127 IAAKYLARKDSRTMALIGNGAQSEFQALAFKALIGVDRIRLYDIDPEATARCSRNLQRFG 186
           +AA++LA  D+  MA+IGNGAQ+EFQALAFKA++G+  I LYDIDP AT +C  NL+  G
Sbjct: 123 VAARHLAPADAHRMAIIGNGAQAEFQALAFKAILGITEISLYDIDPAATRKCVGNLRSHG 182

Query: 187 FQIEACTSAEQAVEGADIITTATADKHNATILSDNMIGPGVHINGVGGDCPGKTEMHRDI 246
           F I    SAE+AV+GA I+TT TADK  ATIL+DNMIG GVHIN +GGDCPGKTE+HRDI
Sbjct: 183 FDIRVANSAEEAVQGAQIVTTVTADKQYATILTDNMIGSGVHINAIGGDCPGKTELHRDI 242

Query: 247 LLRSDIFVEFPPQTRIEGEIQQLAPDHPVTELWRVMTGQDVGRKSDKQITLFDSVGFAIE 306
           LLRS IFVEF PQTRIEGEIQQLAPDHPV+ELW V+ G+  GR S  QITLFDSVGFAIE
Sbjct: 243 LLRSSIFVEFTPQTRIEGEIQQLAPDHPVSELWEVIAGRAEGRTSPDQITLFDSVGFAIE 302

Query: 307 DFSALRYVRDRVEGSSHSSPLDLLADPDEPRDLFGMLLRRQAF 349
           DF+ALRY+RDR+  + H   LD++ADPD+PRDLFGML+R + +
Sbjct: 303 DFAALRYLRDRLADTRHFVELDMIADPDDPRDLFGMLMRAREY 345


Lambda     K      H
   0.320    0.137    0.396 

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: 400
Number of extensions: 6
Number of successful extensions: 1
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: 354
Length of database: 346
Length adjustment: 29
Effective length of query: 325
Effective length of database: 317
Effective search space:   103025
Effective search space used:   103025
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: 49 (23.5 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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