GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Cupriavidus basilensis 4G11

Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate RR42_RS31610 RR42_RS31610 cystathionine beta-lyase

Query= SwissProt::P06106
         (444 letters)



>FitnessBrowser__Cup4G11:RR42_RS31610
          Length = 402

 Score =  143 bits (361), Expect = 9e-39
 Identities = 128/451 (28%), Positives = 195/451 (43%), Gaps = 62/451 (13%)

Query: 1   MPSHFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGY---VYS 57
           M  H DT  +HAG   P    H    VP+  T++  FENS     +      G     Y 
Sbjct: 1   MSHHRDTQLIHAGTP-PFVQGHGPVNVPVVRTSTVRFENSDAYDDIRARHARGERVSSYG 59

Query: 58  RFQNPTSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQ 117
           R    T   LE+ IA LEGG  A    SG AA +L    L   GD+ +    +Y      
Sbjct: 60  RHGMDTHRALEDAIAGLEGGNRAFLAPSGLAAISLTFLALLSPGDHALVVDSVYAPVRRL 119

Query: 118 FKISFKRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHG 177
            +   +R GIE  +    + ++ + +    T+ +YLE+  +  Y V D  ++V IAH+HG
Sbjct: 120 EQTLLRRLGIEVSYFS-PSQDDLDALIRPNTRLLYLESPSSLLYEVLDLPRLVQIAHRHG 178

Query: 178 IPVVVDNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKF 237
           + V  DNT+ A G+  QP+  G DI   ++TK+I GH   + G +V              
Sbjct: 179 VVVATDNTW-ASGHALQPLALGVDISILASTKYISGHSDLMQGAVV-------------- 223

Query: 238 PQFSQPAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAE 297
                        + +EA        H         G  ++   ++L L+G+ TL++R  
Sbjct: 224 -------------VKDEALARRIADAH------DGFGLAISADDAYLALRGIRTLAVRLA 264

Query: 298 RHGENALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADK 357
           +H  NAL +A++LE    V  V YP L S   H    +  S G  G++SF    LP AD 
Sbjct: 265 QHQRNALAVAQFLEAHEAVGRVFYPALPSDPGHALWLRDFS-GANGLVSF---SLPTAD- 319

Query: 358 ETDPFKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGV----TKD 413
                  +  ++VD+L L    A+ G  ++LV         Q+   E+LA        + 
Sbjct: 320 -----VAAARKLVDSLSLFGLGASWGGYESLV---------QVAAPERLAEHSYWRGAEP 365

Query: 414 LIRVSVGIEFIDDIIADFQQSFETVFAGQKP 444
           +IR+ +G+E  +D+IAD  Q          P
Sbjct: 366 VIRLHIGLEAPEDLIADLAQGLAATVQASVP 396


Lambda     K      H
   0.317    0.136    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: 442
Number of extensions: 22
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 444
Length of database: 402
Length adjustment: 32
Effective length of query: 412
Effective length of database: 370
Effective search space:   152440
Effective search space used:   152440
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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