GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Herbaspirillum seropedicae SmR1

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate HSERO_RS19685 HSERO_RS19685 4-aminobutyrate aminotransferase

Query= reanno::Putida:PP_4108
         (416 letters)



>FitnessBrowser__HerbieS:HSERO_RS19685
          Length = 456

 Score =  227 bits (578), Expect = 6e-64
 Identities = 149/415 (35%), Positives = 223/415 (53%), Gaps = 20/415 (4%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTH-YAFNAAP 73
           PI +         D DG  +ID   G+GV ++G CNP VVEAI+ Q+  L H    N++ 
Sbjct: 48  PIAMDQAFGVTFKDPDGNTFIDLSAGVGVSSVGRCNPRVVEAIRKQSESLMHSMEVNSSK 107

Query: 74  HGPYLALMEQLSQFVP--VSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHG 131
                 L  ++S+ +P  +        T  G++A E A+K A+  TG+  IIAF GG+HG
Sbjct: 108 R---TELAAKISEIMPDGLRGDCITFFTQGGSDALEAAVKFAKRVTGRHQIIAFHGGYHG 164

Query: 132 RTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSA-----DTG-VTCEQ-ALKAMDRLFSV 184
              A+  L    A Y++  G   G V H PYP A     DT   + EQ A + +D L + 
Sbjct: 165 IWNASNALTTGTA-YRKGFGPFMGGVIHAPYPYAYRFPFDTSHKSAEQIAGEYVDYLLNT 223

Query: 185 EL-AVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRF 243
              A +DVAA I EPVQGEGG++   P F Q LR+ CD  G L+I+DE+Q+G GRTG+ +
Sbjct: 224 PYTAADDVAAVIVEPVQGEGGYVPPSPEFLQILRKACDRSGALLIVDEVQAGAGRTGKMW 283

Query: 244 AFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303
           A    G++PD+L   K I G MP+  +V R +L A +P G    T++ N IS A AL ++
Sbjct: 284 AVEHSGVKPDMLTFGKGIGGDMPMAGLVMRSDLAAKIPDGSQPNTFAANSISAAVALTNI 343

Query: 304 AQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAP-- 361
           + + D  L          + ++ ER ++   SP++G + G G M GIE      +  P  
Sbjct: 344 SILQDPRLDLVNRAHTLGLEAQ-ERIRSFN-SPWVGEVRGRGLMIGIELVENRETREPLS 401

Query: 362 -AQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
             +L K+M+     G+L++P G+  +++R++  LTI   ++ +GLDI    LA L
Sbjct: 402 REKLGKLMDYVVGHGVLMIPCGRYTNVMRVMPSLTIPRSLMFKGLDIFGAGLASL 456


Lambda     K      H
   0.320    0.137    0.402 

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: 495
Number of extensions: 30
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: 416
Length of database: 456
Length adjustment: 32
Effective length of query: 384
Effective length of database: 424
Effective search space:   162816
Effective search space used:   162816
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.

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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