GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Mesorhizobium ciceri WSM1271

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate YP_004140539.1 Mesci_1329 acetyl-CoA acetyltransferase

Query= SwissProt::Q8VPF1
         (401 letters)



>NCBI__GCF_000185905.1:YP_004140539.1
          Length = 392

 Score =  316 bits (810), Expect = 7e-91
 Identities = 183/400 (45%), Positives = 254/400 (63%), Gaps = 11/400 (2%)

Query: 1   MSREVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQ 60
           MS  + I  A RTP+G F G+ AA  A +L AV ++ L+ R   V+  ++DEV LG    
Sbjct: 1   MSASIVIASAARTPVGSFNGAFAATPAHELGAVVIRELLSR-AGVEPGEVDEVILGQVLT 59

Query: 61  AGEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVES 120
           A +  +N AR A + AGLP       LN++C SG+ A+    + IA G+A ++IAGG ES
Sbjct: 60  AAQ-GQNPARQASINAGLPKETTAWGLNQVCGSGLRAIALGMQQIAIGDARVIIAGGQES 118

Query: 121 MSRAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRA 180
           MS + +             K+ DT I     + L  A  G   M  TA+NVA  ++++R 
Sbjct: 119 MSLSTHAQHLRAGVKMGDFKLIDTMIK----DGLWDAFNGYH-MGNTAENVARQFQITRE 173

Query: 181 DQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKP 240
           DQD FAL SQ  A  AQ AG F +EIV V IKGKKG+T+VD DE++R   T++A+ KLKP
Sbjct: 174 DQDQFALASQNKAEAAQKAGKFKDEIVAVTIKGKKGDTIVDQDEYIRHGATIDAMTKLKP 233

Query: 241 VNGPDKTVTAGNASGVNDGSV-ALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGP 299
               D TVTA NASG+NDG+  AL+++ AEAV++ G+   A+++  A+AGV P++MG GP
Sbjct: 234 AFDKDGTVTAANASGINDGAAGALLMSEAEAVRR-GITPLARIVSWATAGVDPQIMGTGP 292

Query: 300 VPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPL 359
           +PA RK LE+   SV D D++E NEAFAAQ  AV +++G   D + VN NGGAIA+GHP+
Sbjct: 293 IPASRKALEKAGWSVGDLDLVEANEAFAAQACAVNKDMGW--DPSIVNVNGGAIAIGHPI 350

Query: 360 GASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVE 399
           GASGAR+  T V ++ + G ++GL T+C+G G GVA+ VE
Sbjct: 351 GASGARVFNTLVFEMRRRGAKKGLATLCIGGGMGVAMCVE 390


Lambda     K      H
   0.317    0.134    0.379 

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: 416
Number of extensions: 19
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: 401
Length of database: 392
Length adjustment: 31
Effective length of query: 370
Effective length of database: 361
Effective search space:   133570
Effective search space used:   133570
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