GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lysN in Azospirillum brasilense Sp245

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate AZOBR_RS19025 AZOBR_RS19025 acetylornithine aminotransferase

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



>lcl|FitnessBrowser__azobra:AZOBR_RS19025 AZOBR_RS19025
           acetylornithine aminotransferase
          Length = 389

 Score =  185 bits (470), Expect = 2e-51
 Identities = 139/407 (34%), Positives = 202/407 (49%), Gaps = 39/407 (9%)

Query: 16  ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75
           I    G    ++ TDG+R++DF  G+ V  LGH NP +VEA+ AQA +L H + N     
Sbjct: 14  IVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTS-NLFRVA 72

Query: 76  PYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDGGF 129
              +L ++L++    ++      TNSGAEA E   K+ R      G   +  II F+  F
Sbjct: 73  GQESLAKRLTE---ATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQAF 129

Query: 130 HGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVE 189
           HGRTLA ++     A  ++++ +  GP+                 L     L +V  AV 
Sbjct: 130 HGRTLAAVS-----AAQQEKLIKGFGPLLD------------GFDLVPFGDLEAVRNAVT 172

Query: 190 DVAAFI-FEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248
           D  A I  EP+QGEGG  A    F + LR  CDE G+L+ +DEIQ G GRTG+ FA    
Sbjct: 173 DETAGICLEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWA 232

Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308
           GI PD++ +AK I GG PLGA +  ++  + +  G  G TY GNP++ A   A L ++ +
Sbjct: 233 GITPDVMAVAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLE 292

Query: 309 ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVM 368
                  +R    +  R     A   + + G + G G M G+    A G         V+
Sbjct: 293 PGFLDHVQRIGGLLQDRLAGLVAENPAVFKG-VRGKGLMLGLACGPAVGD--------VV 343

Query: 369 EAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
            A RA GLL +P+G   +++RLL PL I    +EE + IL +   EL
Sbjct: 344 VALRANGLLSVPAGD--NVVRLLPPLNIGEAEVEEAVAILAKTAKEL 388


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: 454
Number of extensions: 20
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 416
Length of database: 389
Length adjustment: 31
Effective length of query: 385
Effective length of database: 358
Effective search space:   137830
Effective search space used:   137830
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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