GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Rhodanobacter denitrificans 2APBS1

Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_015446959.1 R2APBS1_RS03900 3-oxoadipyl-CoA thiolase

Query= reanno::Marino:GFF2751
         (415 letters)



>NCBI__GCF_000230695.2:WP_015446959.1
          Length = 400

 Score =  479 bits (1233), Expect = e-140
 Identities = 249/405 (61%), Positives = 304/405 (75%), Gaps = 7/405 (1%)

Query: 7   LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66
           +  A++VDA RTP GR GGAL+ VRADDL A+PI AL  R+P LDW+ +D+V+ GCANQA
Sbjct: 1   MTSAWLVDATRTPFGRLGGALAGVRADDLAALPIAALMARHPTLDWAALDEVILGCANQA 60

Query: 67  GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126
           GEDNR+VARM+ LLAGLP  VP  T+NRLC SG++A+G AARAI  GE +L++AGGVESM
Sbjct: 61  GEDNRNVARMATLLAGLPQSVPAVTVNRLCASGLEAIGQAARAIACGEAELVVAGGVESM 120

Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRED 186
           SRAP+V+ KAD A++R  ++ DTT+GWR VNP ++  YGIDSM +TAEN+A + GI R+ 
Sbjct: 121 SRAPYVLAKADVAYARGQQLEDTTLGWRLVNPRMQAGYGIDSMTQTAENLAREHGIDRDS 180

Query: 187 QDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPR-ETSLEKLASLPT 245
           QDA+ALRSQQRTA AQ +G LA EIT V  P  K+  LVV  DEHPR +T+  KLA+L  
Sbjct: 181 QDAYALRSQQRTAHAQAQGWLAEEITAVHAPHGKES-LVVQVDEHPRADTTAAKLAALKP 239

Query: 246 PFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPA 305
                 ++TAGNASG+NDGA A+LLA   AL +Y L+P AR+V MA AGV PR+MG GP 
Sbjct: 240 LLGAGSSITAGNASGLNDGAAAVLLASEAALARYGLQPLARIVGMAAAGVAPRVMGIGPV 299

Query: 306 PATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLG 365
           PA  K+LA  GL  +D D IE+NEAFAAQ LA TR LGLPDDAEHVN NGGAIALGHPLG
Sbjct: 300 PAIHKLLARTGLGASDFDRIEINEAFAAQVLACTRSLGLPDDAEHVNANGGAIALGHPLG 359

Query: 366 MSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIER 410
            SGARL  TA   L RRH    +   AL ++C+GVGQG+AL +ER
Sbjct: 360 ASGARLALTAAFAL-RRH----RQHRALVSLCVGVGQGLALALER 399


Lambda     K      H
   0.318    0.133    0.382 

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: 514
Number of extensions: 25
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: 415
Length of database: 400
Length adjustment: 31
Effective length of query: 384
Effective length of database: 369
Effective search space:   141696
Effective search space used:   141696
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 (21.7 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