GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Collimonas arenae Ter10

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_061532096.1 CAter10_RS02100 acetyl-CoA C-acyltransferase family protein

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



>NCBI__GCF_001584165.1:WP_061532096.1
          Length = 396

 Score =  255 bits (651), Expect = 2e-72
 Identities = 170/406 (41%), Positives = 226/406 (55%), Gaps = 33/406 (8%)

Query: 3   EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGA 62
           E VIV  ART IG +Y GAL       L   A++ A  RAG+DP +   ++ G  +   A
Sbjct: 6   EVVIVGAARTAIG-SYGGALKDFAPGELGAIAVKEAFARAGVDPLQAGQIIFGNVIHTEA 64

Query: 63  TGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISL 122
               ++R   L AG+   +   T++R C SGLQAI  AA ++     ++AVGGG ES+S 
Sbjct: 65  RDMYVSRVVGLNAGMGKESTALTLNRLCGSGLQAIITAANAIQLGETDVAVGGGVESMSR 124

Query: 123 VQ--------NDKMNTFHAVDPALEAIK---GDVYMAMLDTAETVAKRYGISRERQDEYS 171
                       +M     VD  + A+    G  +M +  TAE VA++YGISRE QD ++
Sbjct: 125 SMYATQAARWGARMGDIKMVDMMVGALSDPFGAGHMGI--TAENVAEKYGISREEQDAFA 182

Query: 172 LESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITL-SQDEGPRPETTAEGL 230
           LESQRR  AA   G F  +I P+  K           + K +TL   DE P+ + T E L
Sbjct: 183 LESQRRATAAIAAGHFKSQIVPVEIK-----------TRKGVTLFDTDEYPKADATMESL 231

Query: 231 AGLK-AVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGC---E 286
           A LK A + EG T+TAGNAS ++DGA+A V+M+   AA  GLKPL     +VSYG    +
Sbjct: 232 AKLKPAFKKEGGTVTAGNASGINDGAAACVLMAADAAAQAGLKPLA---RVVSYGVAGVD 288

Query: 287 PDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAI 346
           P  MG GP+ AV   LKR GL + D+ + E NEAFA Q L     LG+DP   NVNGGAI
Sbjct: 289 PTIMGTGPIPAVQLALKRAGLHLSDMEVIESNEAFAAQSLGVCKGLGLDPALTNVNGGAI 348

Query: 347 SVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392
           ++GHP G SGA +A   L E  R   +Y ++TMC+GGG G A + E
Sbjct: 349 ALGHPLGASGAIIAVKCLYELIRTNKRYGLITMCIGGGQGIALIIE 394


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: 478
Number of extensions: 22
Number of successful extensions: 3
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: 396
Length adjustment: 31
Effective length of query: 364
Effective length of database: 365
Effective search space:   132860
Effective search space used:   132860
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