GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimB in Herbaspirillum seropedicae SmR1

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate HSERO_RS01265 HSERO_RS01265 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS01265 HSERO_RS01265 acetyl-CoA
           acetyltransferase
          Length = 398

 Score =  296 bits (757), Expect = 9e-85
 Identities = 180/398 (45%), Positives = 238/398 (59%), Gaps = 8/398 (2%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRA-GIDPKEVEDVVMGAAMQ 59
           + +A IV+  RTPIGKA RG    T    LL  AI+ AV +  G+DPK +ED ++G +  
Sbjct: 5   LQDAYIVAATRTPIGKAPRGMFKNTRPDDLLVRAIQSAVAQVPGLDPKLIEDAIVGCSFP 64

Query: 60  QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119
           +GA G N+AR A+L AGLP T  G TI+R CASG+ AIA+AA  +     ++ +  G ES
Sbjct: 65  EGAQGLNMARNAVLLAGLPNTIGGVTINRYCASGITAIAMAADRIRVGEADVMIAAGAES 124

Query: 120 ISLVQNDKMNTFHAVDPALEAIKGD-VYMA--MLDTAETVAKRYGISRERQDEYSLESQR 176
           +S+V    M  FH     + A K + V MA  M  TAE VA+++ +SRE QDE+SL S +
Sbjct: 125 MSMVP---MMGFHP-SININAFKDENVGMAYGMGLTAEKVAQQWKVSREAQDEFSLASHQ 180

Query: 177 RTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAV 236
           +  AAQ+ G+F DE+          + ATG +  K  T+S DEGPR ++    LA LK V
Sbjct: 181 KAIAAQEAGEFADEMTSFEIVERFPNLATGEIDVKTRTVSLDEGPRADSNLAALAKLKPV 240

Query: 237 RGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVF 296
                ++TAGN+SQ SDGA A +I+S+K      L PL  F      G  P+ MGIGP  
Sbjct: 241 FAAKGSVTAGNSSQTSDGAGALIIVSEKILKQFNLTPLARFVSFAVRGVPPEIMGIGPKE 300

Query: 297 AVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSG 356
           A+P  LK  GL+ D I   ELNEAFA Q L     LG+DP K+N  GGAI++GHP G +G
Sbjct: 301 AIPAALKAGGLTQDQIDWIELNEAFAAQALAVIGDLGLDPSKVNPMGGAIALGHPLGATG 360

Query: 357 ARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           A  A   +   RR+  KY +VTMCVG GMG+AG+FE V
Sbjct: 361 AIRAATTIHALRRKNLKYGMVTMCVGTGMGAAGIFERV 398


Lambda     K      H
   0.316    0.134    0.378 

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: 395
Number of extensions: 20
Number of successful extensions: 3
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: 395
Length of database: 398
Length adjustment: 31
Effective length of query: 364
Effective length of database: 367
Effective search space:   133588
Effective search space used:   133588
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 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