GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argI in Dinoroseobacter shibae DFL-12

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate 3609708 Dshi_3091 aspartate carbamoyltransferase (RefSeq)

Query= curated2:A8LE44
         (317 letters)



>FitnessBrowser__Dino:3609708
          Length = 316

 Score =  103 bits (257), Expect = 5e-27
 Identities = 98/316 (31%), Positives = 143/316 (45%), Gaps = 25/316 (7%)

Query: 1   MTARHFLLDTDLTSSEQAALLDLADQLKATRRDRKPARRPLEGRSVALIFEKPSTRTRLS 60
           + ARH L    L   E   LLDLAD+     R        L+G +   +F + STRT+ S
Sbjct: 3   LRARHLLGIEHLAPDEIVTLLDLADRYADLNRRPDKHGDALDGLTQINMFFENSTRTQAS 62

Query: 61  FDVAVAELGGHPIVIDSGSSQLGRGETIEDTAAVL-SRYVDAIVIRTFAQDRVDRMAAAA 119
           F++A   LG   + ++  +S + +GET+ DTA  L + + D +V+R      V+ +A   
Sbjct: 63  FEIAGKRLGADVMNMEVRASSIKKGETLIDTAMTLNAMHPDLLVVRHPHSGAVNLLAEKV 122

Query: 120 TVPVINALSD-HTHPCQALADLQTIREIRGRLAGVTLAYLGDGNNVAHS------LLLAG 172
              V+NA    H HP QAL D  TIR  +G+L  + +A  GD   +AHS      +LL G
Sbjct: 123 NCAVLNAGDGRHEHPTQALLDALTIRRAKGKLHRLNVAICGD---IAHSRVARSNILLLG 179

Query: 173 ALAGLRVHVASPPGYEPIEQVVRHANEIGAVTGGEALVTHDALEAAAGADVLYTDVWASM 232
            +   R+ +  P    P E       E+G        V  D      G DV+        
Sbjct: 180 KMEN-RIRLVGPRTLMPAE-----IAELGVE------VYEDMKAGLDGVDVVMMLRLQKE 227

Query: 233 GQDTE-SDSRALVFQPYRLDEKVVEAASPDAIVMHCLPAHREMEISAAVLDG-PRSVVFD 290
             D     S    +  Y LD + +  A PDAIVMH  P +R +EI   + D   RSV+ +
Sbjct: 228 RMDGGFIPSEREYYHRYGLDAEKLAYAKPDAIVMHPGPMNRGVEIDGTLADDINRSVIQE 287

Query: 291 QAENRLHAQKALLSFL 306
           Q E  +  + A +  L
Sbjct: 288 QVEMGVAVRMAAMDLL 303


Lambda     K      H
   0.318    0.132    0.371 

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: 235
Number of extensions: 11
Number of successful extensions: 3
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: 317
Length of database: 316
Length adjustment: 27
Effective length of query: 290
Effective length of database: 289
Effective search space:    83810
Effective search space used:    83810
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: 48 (23.1 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