GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Herbaspirillum seropedicae SmR1

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate HSERO_RS16670 HSERO_RS16670 acetylornithine aminotransferase

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



>FitnessBrowser__HerbieS:HSERO_RS16670
          Length = 400

 Score =  179 bits (455), Expect = 1e-49
 Identities = 132/416 (31%), Positives = 207/416 (49%), Gaps = 53/416 (12%)

Query: 16  ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHY--AFNAAP 73
           +  + G    + D +GKRY+D++ G  V  LGH    + +A+ AQ+ +L +   AF   P
Sbjct: 20  LVFTEGHGMWLTDHNGKRYLDYLQGWAVNTLGHAPQCIADALAAQSKKLINPSPAFYNEP 79

Query: 74  HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR---------GATGKRAIIA 124
                 L+   S F  V +       NSG EA E A+K+AR           + +  II 
Sbjct: 80  SIELAKLLTANSVFDRVFF------ANSGGEANEGAIKLARKWGKKNPAADGSARFEIIT 133

Query: 125 FDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSV 184
           F   FHGRTLAT++ +GK         ++PG      +P A            ++ L SV
Sbjct: 134 FKHSFHGRTLATMSASGKDGWDTMFAPQVPG------FPKA-----------VLNDLESV 176

Query: 185 ELAV-EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRF 243
           +  + E   A + EPVQGEGG +     F Q LR    E+ +L+I+DE+QSG GRTGQ F
Sbjct: 177 KALIGEHTVAVMLEPVQGEGGVIPASKEFMQGLRSLTKEKNLLLIVDEVQSGMGRTGQLF 236

Query: 244 AFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303
           A+   GIEPD++ LAK I GG+PL A++ R+E+ A    G  GGTY+GNP+  A  +A +
Sbjct: 237 AYQHSGIEPDIMTLAKGIGGGVPLAALLAREEI-ACFEAGEQGGTYNGNPLMTAVGVAVI 295

Query: 304 AQMTD----ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSP 359
            ++      E++   G+   Q  +   E++   G         G G +R ++    D  P
Sbjct: 296 KELLKPGFMESVRERGQYLRQRSLEISEKYGFEG-------ERGEGLLRALQLGR-DIGP 347

Query: 360 APAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
              + A+ +E     GLLL  +    +++R +  L +  E +++   +LE+ LA++
Sbjct: 348 QIVEAARNLEPV---GLLL--NSPRPNLLRFMPALNVTKEEIDQMFSMLEEVLAKI 398


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: 406
Number of extensions: 17
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: 416
Length of database: 400
Length adjustment: 31
Effective length of query: 385
Effective length of database: 369
Effective search space:   142065
Effective search space used:   142065
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.

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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