GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS01265
          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:

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