GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Herbaspirillum seropedicae SmR1

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate HSERO_RS12060 HSERO_RS12060 indole acetamide hydrolase

Query= curated2:A7NKM0
         (490 letters)



>FitnessBrowser__HerbieS:HSERO_RS12060
          Length = 468

 Score =  223 bits (568), Expect = 1e-62
 Identities = 167/491 (34%), Positives = 242/491 (49%), Gaps = 41/491 (8%)

Query: 4   LYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARR 63
           L  +T+ + R+ L+    S LE  DAL+    A +  +  +L  D    R+QAR  D + 
Sbjct: 3   LVDMTLIEVRQGLSDRRFSCLEYVDALIAETEA-QWDLNCYLQRDPEQLRSQARMLDEQ- 60

Query: 64  AAGDASPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKLN 123
             G   PL GIP+ IKD I   G+ +T  +  L N  P   AT V  L  AGA+  GK N
Sbjct: 61  --GGHGPLSGIPIAIKDNIDVAGIASTAGTAALRNNVPQRHATVVEYLFGAGALHAGKAN 118

Query: 124 CDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQPA 183
             E A G +  N  F   RNP++ E + GGSSGG  A +AA  APAA+GTDTGGS+R PA
Sbjct: 119 MHELAFGITNNNGVFGPCRNPYDAELIAGGSSGGCGALLAARLAPAAVGTDTGGSVRIPA 178

Query: 184 ALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTDY 243
           ALCG+ GL+PT  R S++G+V  + + D  GPMAR+V D A++ +++AG           
Sbjct: 179 ALCGVVGLRPTSRRYSQHGVVPISHTRDTPGPMARSVADVALLDQIMAG----------- 227

Query: 244 PAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPH-T 302
            + D    L      LR+GV R     G++ +VEA    A+  LRE G E+ ++ LP   
Sbjct: 228 -SRDSAPLLALPPSQLRLGVLRNPSWQGLEEEVEANANAALMQLREAGVELVDVDLPTLA 286

Query: 303 PYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRIMLGT 362
           P +    + I   E   +L  +        +      D ++R       P+V R I    
Sbjct: 287 PLSHAAGFAIVLHEFLIDLPAY--------LQASDARDVIKRVLAEVGSPDVARIIQA-- 336

Query: 363 YALSAGYYDAYYKRAQQVRTLIRRDYQQAF--EQVDVIAAPTTPTVAFKIGAHTDDPLAM 420
             L     +  Y+ A + R  ++  Y+  F  + VD +  PTT   A  +G   DD +A+
Sbjct: 337 -TLDQPVPEHAYRLALEQRRTMQALYRDCFRSQGVDALIFPTTALTARPLG--EDDTVAL 393

Query: 421 YLEDVCTLP--------LNLAGLPGLVVPCGFAE-GLPIGLQLIGRAFDEESLLRVGDAY 471
             E V T P         ++AGLP + +P G +E GLP+GL+L G    +  LL+V  + 
Sbjct: 394 RGERVPTFPAFARNADGASIAGLPSISIPVGLSEYGLPVGLELDGPEGSDRRLLQVAASL 453

Query: 472 QRVTDWHTRMP 482
           + V     R P
Sbjct: 454 ETVLGRGPRPP 464


Lambda     K      H
   0.320    0.136    0.398 

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: 488
Number of extensions: 24
Number of successful extensions: 4
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: 490
Length of database: 468
Length adjustment: 34
Effective length of query: 456
Effective length of database: 434
Effective search space:   197904
Effective search space used:   197904
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: 51 (24.3 bits)

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

Links

Downloads

Related tools

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