GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Phaeobacter inhibens BS107

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate GFF1992 PGA1_c20260 amidase-like protein

Query= curated2:Q72L58
         (471 letters)



>FitnessBrowser__Phaeo:GFF1992
          Length = 474

 Score =  200 bits (508), Expect = 1e-55
 Identities = 163/489 (33%), Positives = 236/489 (48%), Gaps = 56/489 (11%)

Query: 3   AHEIRARVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLNER--LLEEAEAVDPGL---P 57
           A E    ++ G  + + + +  L R+  L+P L A ++L +R  LL EA A D      P
Sbjct: 8   ARETLQAISAGRRTAVALMEETLARIDALNPSLNAIVALRDREVLLAEAAAADRSTTRGP 67

Query: 58  LAGLVVAVKDNIATRGLRTTAGSRLLENFVPPYEATAVARLKALGALVLGKTNLDEFGMG 117
           L GL +A+KD     G+R+T GS LL +FVP  +   VARL+A GAL +GKTN  EFG+G
Sbjct: 68  LHGLPMAIKDLANVAGVRSTQGSPLLADFVPQQDDLMVARLRAAGALFIGKTNTPEFGLG 127

Query: 118 SSTEHSAFFPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAFCGVYG 177
           S T +     T NP+D  R  GGSSGG+A ALA  +  LA GSD  GS+R PA +C VYG
Sbjct: 128 SHTFNPVHGATANPYDHSRSCGGSSGGAAVALATGMVALADGSDMMGSLRNPAGWCNVYG 187

Query: 178 LKPTYGRV---SRFGLIAYASSLDQIGPMARSVRDLALLMDAVAGPDPLDATSLDLPPRF 234
            +P++GRV    R  L  +  S +  GPMAR   DLALL+D ++G DP    +       
Sbjct: 188 FRPSWGRVPGEPRGDLFLHPLSTN--GPMARCPEDLALLLDVMSGSDPRQPLAATAGAGR 245

Query: 235 QEALEGPLP---PLRLGVVREALAGNSP---GVERALEEALKVFRELGLSVREVSWPSLP 288
           + +   PLP   P+R+G + +   G  P   G+    E AL+  R LG  V  ++ P   
Sbjct: 246 RVS---PLPEARPMRIGWLAD-WGGAYPMETGILETCETALETLRTLGHQVETLAPPFAA 301

Query: 289 QAL-AAYYILAPAEASSNLARYDGTLYGRRAEGEEVEGMMEATRALFGLEVKRRVLVGTF 347
           + +  ++  L     +S L  + G +   +   +  +  +++  AL G E++        
Sbjct: 302 ERIWQSWSTLRSFSVASGLRVFGGQMQQLK---DSAQWELQSGLALSGQEIQ-------- 350

Query: 348 VLSSGYYEAYYGRAQAFRRRLKAEAQALFREVDLLLLPTTPHPAFPFGARRDPLAMYRE- 406
                        A   R   +  A  LF + D L+LPT     +PF    D   +  E 
Sbjct: 351 ------------AASDLRSDWQRVAARLFSQYDALVLPTA--QCWPFDIALDYPQVIGET 396

Query: 407 --DLY------TVGANLTGLPALSFPAGF-EGHLPVGLQLLAPWGEDERLLRAALAFEEA 457
             D Y          +L G+P L+ PAGF    LP+G+Q+ A  G D  LL     +  A
Sbjct: 397 AMDSYHRWMEVVTPVSLIGVPCLAAPAGFGPAGLPMGIQIFAAHGRDRELLALGQQYHWA 456

Query: 458 TARAHLKAP 466
           T     + P
Sbjct: 457 TRWPERRPP 465


Lambda     K      H
   0.319    0.137    0.395 

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: 503
Number of extensions: 22
Number of successful extensions: 5
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: 471
Length of database: 474
Length adjustment: 33
Effective length of query: 438
Effective length of database: 441
Effective search space:   193158
Effective search space used:   193158
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 (21.7 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