GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Pseudomonas putida KT2440

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate PP_4223 PP_4223 diaminobutyrate-2-oxoglutarate transaminase

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



>FitnessBrowser__Putida:PP_4223
          Length = 452

 Score =  202 bits (513), Expect = 2e-56
 Identities = 150/426 (35%), Positives = 210/426 (49%), Gaps = 34/426 (7%)

Query: 3   QESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQA--- 59
           QES ++S     P+ L   R   V D +G+++ID + G G L LGH +P VVEAIQ    
Sbjct: 20  QESNARSYPRRIPLALRRARGIHVEDVEGRQFIDCLAGAGTLALGHNHPVVVEAIQRVLA 79

Query: 60  -----QATRLTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR 114
                    LT    +      +  L E L +   V +        +G +A E ALK+ R
Sbjct: 80  DELPLHTLDLTTPVKDRFVQDLFGILPEALRREAKVQF-----CGPTGTDAVEAALKLVR 134

Query: 115 GATGKRAIIAFDGGFHGRTLATLNLNGKVAPYKQRVGELPGP-VYHLPYP---SADTGVT 170
            ATG+  ++AF G +HG +   LNL G   P KQ +G L G  V  +PYP       G+ 
Sbjct: 135 TATGRSTVLAFQGAYHGMSQGALNLMGSHGP-KQPLGALLGNGVQFMPYPYDYRCPFGLG 193

Query: 171 CEQALKAM-----DRLFSVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGI 225
            E  +KA      + L   E  V   AA I E VQGEGG +  D  + + +RR  ++ G+
Sbjct: 194 GEAGVKANLHYLENLLLDPESGVPLPAAVILEVVQGEGGVVPADIEWLKGVRRITEQAGV 253

Query: 226 LIIIDEIQSGFGRTGQRFAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGL 285
            +I+DEIQSGF RTG+ FAF   GI PD++ L+K+I G +PL  VV R  L    P G  
Sbjct: 254 ALIVDEIQSGFARTGRMFAFEHAGIVPDVVTLSKAIGGSLPLAVVVYRDWLDTWKP-GAH 312

Query: 286 GGTYSGNPISCAAALASLAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVG 345
            GT+ GN ++ AA  A +  + +  LA   E   Q +    +R +     P +G + G G
Sbjct: 313 AGTFRGNQMAMAAGSAVINYLVEHRLAEHAEAMGQRLRGHLQRLQRD--YPQLGDIRGRG 370

Query: 346 AMRGIEFANADGS-------PAPAQLA-KVMEAARARGLLLMPSGKARHIIRLLAPLTIE 397
            M G+E  +  G        PA   LA KV      RGL+L   G+   ++R L PL I 
Sbjct: 371 LMLGVELVDPQGQPDALGHPPANRDLAPKVQRECLKRGLILELGGRHGAVVRFLPPLIIS 430

Query: 398 AEVLEE 403
           AE ++E
Sbjct: 431 AEQIDE 436


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: 500
Number of extensions: 28
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: 452
Length adjustment: 32
Effective length of query: 384
Effective length of database: 420
Effective search space:   161280
Effective search space used:   161280
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