GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Sphingomonas indica Dd16

Align alanine racemase (EC 5.1.1.1) (characterized)
to candidate WP_085217314.1 B9N75_RS02160 cystathionine beta-lyase

Query= BRENDA::P06721
         (395 letters)



>NCBI__GCF_900177405.1:WP_085217314.1
          Length = 407

 Score =  344 bits (882), Expect = 3e-99
 Identities = 189/394 (47%), Positives = 250/394 (63%), Gaps = 11/394 (2%)

Query: 2   ADKKLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGT 61
           +D++ DT +V AGR +++   AVN     AS+++FD+V   + A    A+G  +YGR GT
Sbjct: 20  SDRRRDTTIVQAGRRREWIGAAVNPPTWHASTILFDTVAEMEAAAP--ADGTFYYGRHGT 77

Query: 62  LTHFSLQQAMCELEGGA-GCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSK 120
            T ++L +A+  LE GA G  LFP GAAAVA ++LA +  GD +LM ++AY P++  C  
Sbjct: 78  PTTWALSEALTALEPGAVGTRLFPSGAAAVAMALLAVLRPGDELLMVDSAYGPTRAICDS 137

Query: 121 ILSKLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDA 180
            L +LG+TT ++DPLIGADI   +   T+ +FLESPGS+T EV DVPAIVA  R      
Sbjct: 138 ELKRLGITTRYYDPLIGADIAALIGDKTRAIFLESPGSLTFEVQDVPAIVAVARE--RGI 195

Query: 181 IIMIDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQLRENAYLM 240
             +IDNTWA  + F A+  G+D+SI A TKY+ GHSD M+G+   + R W++LR+   + 
Sbjct: 196 ATLIDNTWATPLFFPAIAAGVDISILACTKYIGGHSDLMMGSVTVSERWWDRLRQVFRMY 255

Query: 241 GQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFW 300
           GQ V  D A   +RGLRTLGVR+ +H  ++L VA WLA  PQVARV HPAL    GH  W
Sbjct: 256 GQAVGPDDAAACARGLRTLGVRMERHQANALTVANWLANQPQVARVLHPALADCPGHALW 315

Query: 301 KRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRP 360
            RDF GSSGLFS +L    +    A  +D    F++ YSWGGYESL +   PE + +  P
Sbjct: 316 SRDFKGSSGLFSIILNGG-DAAARAALIDGLEHFAIGYSWGGYESLAVPADPERLRSATP 374

Query: 361 -QGEIDFSGTLIRLHIGLEDVDDLIADLDAGFAR 393
            Q E    G L+RLHIGLED DDLI DL  G AR
Sbjct: 375 WQAE----GPLVRLHIGLEDPDDLIEDLARGLAR 404


Lambda     K      H
   0.321    0.135    0.402 

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: 431
Number of extensions: 20
Number of successful extensions: 6
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: 395
Length of database: 407
Length adjustment: 31
Effective length of query: 364
Effective length of database: 376
Effective search space:   136864
Effective search space used:   136864
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 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