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_RS20660 HSERO_RS20660 acetyl-CoA acetyltransferase

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



>FitnessBrowser__HerbieS:HSERO_RS20660
          Length = 401

 Score =  238 bits (608), Expect = 2e-67
 Identities = 161/411 (39%), Positives = 222/411 (54%), Gaps = 31/411 (7%)

Query: 3   EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQQG 61
           EA+I    RTP G+ Y GAL A     L    I   ++R  G+D   VED++ G A Q G
Sbjct: 2   EALICDAIRTPFGR-YGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAG 60

Query: 62  ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121
               N+AR A L AGLP+   G+T++R C S L A+ +AAR++    V++ + GG ES++
Sbjct: 61  EDNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMT 120

Query: 122 ---LVQNDKMNTF-------------HAVDPALEAIKGDVYMAMLDTAETVAKRYGISRE 165
               V     + F               V+P ++A  G    +M +TAE VA  + I+R 
Sbjct: 121 RAPFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYG--IDSMPETAENVATDFQINRA 178

Query: 166 RQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPET 225
            QD ++L SQ+R AAAQ  G F  EIAP++      D          + ++ DE PRP+T
Sbjct: 179 DQDAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDP---------LVVTTDEHPRPDT 229

Query: 226 TAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGC 285
           T   LA LK V     T+TAGNAS ++DGA A ++ S K A    LKP     GM + G 
Sbjct: 230 TLATLAKLKGVVRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGV 289

Query: 286 EPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNVNG 343
            P  MG GP  AV ++L + GL++  + + ELNEAFA Q L     LG+  D   +N NG
Sbjct: 290 APRIMGFGPAPAVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNG 349

Query: 344 GAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           GAI++GHP G SGARL   A+ +  R   +YA+ TMC+G G G A + E V
Sbjct: 350 GAIAIGHPLGASGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400


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: 390
Number of extensions: 26
Number of successful extensions: 4
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: 401
Length adjustment: 31
Effective length of query: 364
Effective length of database: 370
Effective search space:   134680
Effective search space used:   134680
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