GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Mesorhizobium ciceri WSM1271

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate YP_004140539.1 Mesci_1329 acetyl-CoA acetyltransferase

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



>NCBI__GCF_000185905.1:YP_004140539.1
          Length = 392

 Score =  251 bits (642), Expect = 2e-71
 Identities = 151/393 (38%), Positives = 219/393 (55%), Gaps = 21/393 (5%)

Query: 5   VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGATG 64
           VI S ARTP+G ++ GA  AT    L    I   + RAG++P EV++V++G  +   A G
Sbjct: 6   VIASAARTPVG-SFNGAFAATPAHELGAVVIRELLSRAGVEPGEVDEVILGQVLT-AAQG 63

Query: 65  GNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISLVQ 124
            N AR+A + AGLP  T    +++ C SGL+AIAL  + +      + + GG ES+SL  
Sbjct: 64  QNPARQASINAGLPKETTAWGLNQVCGSGLRAIALGMQQIAIGDARVIIAGGQESMSLST 123

Query: 125 ND-------KMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYSLESQ 175
           +        KM  F  +D  ++    D +    M +TAE VA+++ I+RE QD+++L SQ
Sbjct: 124 HAQHLRAGVKMGDFKLIDTMIKDGLWDAFNGYHMGNTAENVARQFQITREDQDQFALASQ 183

Query: 176 RRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKA 235
            +  AAQ+ GKF DEI  ++ K              D  + QDE  R   T + +  LK 
Sbjct: 184 NKAEAAQKAGKFKDEIVAVTIKG----------KKGDTIVDQDEYIRHGATIDAMTKLKP 233

Query: 236 VRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPV 295
              +  T+TA NAS ++DGA+  ++MS+  A  +G+ PL       + G +P  MG GP+
Sbjct: 234 AFDKDGTVTAANASGINDGAAGALLMSEAEAVRRGITPLARIVSWATAGVDPQIMGTGPI 293

Query: 296 FAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMS 355
            A  + L++ G SV D+ L E NEAFA Q       +G DP  +NVNGGAI++GHP G S
Sbjct: 294 PASRKALEKAGWSVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGAS 353

Query: 356 GARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388
           GAR+    + E RRR AK  + T+C+GGGMG A
Sbjct: 354 GARVFNTLVFEMRRRGAKKGLATLCIGGGMGVA 386


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: 418
Number of extensions: 21
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 395
Length of database: 392
Length adjustment: 31
Effective length of query: 364
Effective length of database: 361
Effective search space:   131404
Effective search space used:   131404
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 24 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