GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Pseudomonas simiae WCS417

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate GFF3456 PS417_17690 amidase

Query= curated2:Q6A8P5
         (501 letters)



>FitnessBrowser__WCS417:GFF3456
          Length = 467

 Score =  196 bits (498), Expect = 1e-54
 Identities = 159/482 (32%), Positives = 224/482 (46%), Gaps = 43/482 (8%)

Query: 1   MNELLTLTAAELGERIAARQISSEEVTQAHLDRISEVDGDIHAFLLVDHAGALDAARRID 60
           M+E+  LTA +L +    + +S  +VT+  L RI   +  ++A+  VD  GAL+AAR  +
Sbjct: 1   MSEIGQLTAVQLLQHFRDKTLSPVDVTEDALLRIERYNPVVNAYCHVDPEGALNAARASE 60

Query: 61  ARIADGEHLGPLAGVPLAVKDLFCTKGIATTASSQMLEGWIP-PYDSTIVTRCKDAGMVI 119
            R  +G+  G L GVP ++KDL  T G+ T   S+      P   D+      + AG V+
Sbjct: 61  QRWLNGQPCGALDGVPASIKDLTLTVGMPTRKGSRTTSAEGPWDVDAPFTAFMRKAGAVL 120

Query: 120 LGKTNLDEFAMGSSTETSAFGPTHNPWDLERVPGGSGGGSAASLASFQAPLALGTDTGGS 179
           LGKT   EF     T+   +G T NPWD     GGS GG+ A+ A     L  G+D GGS
Sbjct: 121 LGKTTTPEFGWKGVTDNPLYGITRNPWDTRTTAGGSSGGAGAAAALNLGVLHQGSDAGGS 180

Query: 180 IRQPGAVTGTVGIKPTYGSTSRYGVIAMASSLDTPGPCARTVLDAALLHQAIAGHDAMDQ 239
           IR P A TGT GIKPT+G   ++   AM + L   GP  R V D+ L+ Q IA  DA D 
Sbjct: 181 IRIPCAFTGTFGIKPTFGYVPQWPASAM-TLLSHLGPMTRKVEDSVLMLQTIAQPDARD- 238

Query: 240 TTINQP--TPAVVEAARQTDVSGVRIGVVTELSGQVYDPQVEARFHEAVEMLIEAGAEVV 297
             I  P  TP +      TD++G+R+           DPQV     +AV  L++ GA V 
Sbjct: 239 GLIGAPRTTPWLTPG---TDLNGLRVAYSPNFGYVDVDPQVAKVVAQAVAGLVQLGAHVE 295

Query: 298 EVSCPNFDLALPAYYLIQPAEVSSNLARYDAMRYGLRVNDDGEHSAEQ--VMRATRGAGL 355
           ++  P F           P EV S L    A R    +ND  +   +   +  A RG  L
Sbjct: 296 QID-PGFS---------DPLEVFSTLWAAGAARLTRPMNDAQKQLLDPGLLRIAQRGERL 345

Query: 356 GAEAKRRIILGTYALSAGYYDAYYGSAQKVRTLIQRDFEKAWQMCDVLVSPATPTTAFRL 415
             +                    + +A + R  +        +  DVLVSP  P TAF  
Sbjct: 346 SLDD-------------------FNAALEARAALVARMAAFHEHYDVLVSPMMPITAFDA 386

Query: 416 GERTADPMAMY---RSDLCTVPANMAGSPAGSFPIGLSETDGMPVGMQVMAPIMADDRIY 472
           G        +    +    T P N+   PA S P GL+ T+G+PVG+ V+    AD+++ 
Sbjct: 387 GHDVPPGSGLQEWTQWTPFTYPFNLTQQPAASVPCGLA-TNGLPVGLHVVGARFADEQVL 445

Query: 473 RV 474
           RV
Sbjct: 446 RV 447


Lambda     K      H
   0.317    0.133    0.387 

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: 564
Number of extensions: 35
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: 501
Length of database: 467
Length adjustment: 34
Effective length of query: 467
Effective length of database: 433
Effective search space:   202211
Effective search space used:   202211
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 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