GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Sinorhizobium meliloti 1021

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate SMc02413 SMc02413 aminotransferase

Query= curated2:A0QYS9
         (390 letters)



>FitnessBrowser__Smeli:SMc02413
          Length = 437

 Score =  217 bits (553), Expect = 4e-61
 Identities = 151/406 (37%), Positives = 213/406 (52%), Gaps = 41/406 (10%)

Query: 19  PLSLVSGEGAVVTDADGREYLDLLGGIAVNLLGHRHPAVIEAVTTQL-DTLGHTSNLYAT 77
           P ++V G GA +T  DGR+ LD         LGH HPA+ EAV   L D  G +    A 
Sbjct: 22  PQAVVGGSGAYLTADDGRQLLDFSASWGAASLGHSHPAIREAVGRALSDQAGASYLSSAN 81

Query: 78  EPGIALAEALVGQLGTQAR--VFFCNSGTEANE-VAFKITRLTGKTKIVAAEGAFHGRTM 134
           E  + LAE L+  +  +AR  V+F +SG++ANE VA  +   TG+ +I+A  GA+HG T+
Sbjct: 82  EACVLLAEKLLSLVPERARGRVWFGHSGSDANETVARIVVAATGRPRILAFHGAYHGGTI 141

Query: 135 GSLALTGQPSKQAP------FEPLPGNVMHVPYGDVAALEAAV------------DDQTA 176
           GS+ ++G P++Q          P P +  +      AA +AA+             ++ A
Sbjct: 142 GSMGVSGHPAQQGSRAEGLTLVPYPNS--YAAGSPEAARDAALAHLERLFATEVPPEEVA 199

Query: 177 AVFLEPIMGEGGVVVPPAGYLVAAREITSKHGALLVLDEVQTGVGRTGAFFAHQHDGIVP 236
           A F+EPI  +GG++VPP G+  A   +  +HG L+V DEV+ G+GR+G F A +H GI P
Sbjct: 200 AFFIEPIQSDGGMLVPPDGFFKAVEALCRRHGILIVSDEVKVGLGRSGRFNAFEHSGIEP 259

Query: 237 DVVTMAKGLGGGLPIGACLAVGATGDLLTPGLHGSTFGGNPVCTAAGLAVLKTLAAEDLV 296
           D+V   KGLGGGLPI A +   A  +  +      T  GNPVC AA LAVL+T+  + L+
Sbjct: 260 DIVVFGKGLGGGLPISAVVGPEAIMN-HSVAFSLQTVHGNPVCAAAALAVLQTIERDHLI 318

Query: 297 ARAGVLGKTLSHGIEEL--GHPLVDKVRGKGLLQGIVLTVPSAKAVETAARDAGFLVNAA 354
             A   GK L   ++ L   H L+  VRG+GL  GI L    A   E A+R A   V  A
Sbjct: 319 LNADRSGKVLREALDRLTARHTLIGDVRGRGLALGIELVTDPASR-EPASRQAALTVYRA 377

Query: 355 ------------APEVVRLAPPLIITEGQIEAFITAL-PAVLDTAA 387
                          V+ L PPL +T  + E+ +  L  A+ D AA
Sbjct: 378 FQLGLVLYYVGVQSNVLELTPPLTLTPAEAESGVAMLGQALADVAA 423


Lambda     K      H
   0.317    0.136    0.391 

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: 526
Number of extensions: 31
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: 390
Length of database: 437
Length adjustment: 31
Effective length of query: 359
Effective length of database: 406
Effective search space:   145754
Effective search space used:   145754
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