GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Magnetospirillum magneticum AMB-1

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_011383657.1 AMB_RS06320 phenylacetate--CoA ligase

Query= BRENDA::B4EL89
         (440 letters)



>NCBI__GCF_000009985.1:WP_011383657.1
          Length = 432

 Score =  477 bits (1227), Expect = e-139
 Identities = 243/430 (56%), Positives = 316/430 (73%), Gaps = 9/430 (2%)

Query: 14  IETASRDELQALQLERLKWSLRHAYDNVPHYRRTFDAAGVHPDDLKSLADLAKFPFSTKN 73
           +E   R  L+ALQL+RL+  L HAY +VPH R  FDAAG+ PDDL+ L DLA+FPF+ K 
Sbjct: 8   VERLDRPALKALQLQRLRDLLSHAYAHVPHTRAAFDAAGIKPDDLRHLEDLARFPFTVKA 67

Query: 74  DLRDNYPFGLFAVPREQVVRVHASSGTTGKPTVVGYTARDIDTWANVTARSIRAAGGRPG 133
           DLRDNYPFGLFAVPRE+VVR+HASSGTTG+PTVVGYT  DID WA + ARS+ A G RPG
Sbjct: 68  DLRDNYPFGLFAVPREKVVRLHASSGTTGRPTVVGYTQADIDIWAGLMARSLAATGIRPG 127

Query: 134 DTLHNAFGYGLFTGGLGIHYGAERLGCMVVPMSGGQTEKQVQLIRDFEPKIILVTPSYML 193
           D +HNA+GYGLFTGGLG HYGAERLGC VVPMSGG TEKQ+ LI DF  + +  TPSY L
Sbjct: 128 DVVHNAYGYGLFTGGLGFHYGAERLGCSVVPMSGGNTEKQIGLISDFGARALAATPSYAL 187

Query: 194 NLIDEMVRQGMDPAESSLKIGIFGAEPWTQALRNEVETRVGIDALDIYGLSEVMGPGVAC 253
           N+ +   + G+  AES L +G+FGAEPW++++R E++ R+GI A D+YGLSE+MGPGVA 
Sbjct: 188 NIAEVAEQMGVSLAESPLAVGVFGAEPWSESMRAELDRRLGIKACDMYGLSEIMGPGVAI 247

Query: 254 ECVETKDGPVIWEDHFYPEIIDPVTGEVLPDGSQGELVFTSLTKEAMPVIRYRTRDLTAL 313
           EC E + G   WEDHF  E++DP T E LP G++GELV T+LTK+A+P++RYRTRD+T L
Sbjct: 248 EC-EHRVGLHGWEDHFLFEVVDPETLEPLPMGAEGELVITTLTKQALPMVRYRTRDITRL 306

Query: 314 L-PPTA--RAMRRLAKITGRSDDMLIVRGVNVFPSQIEEIVVALPLLSGQFQITLSRDGH 370
              P A  R   R+ ++TGR+DDM+I+RGVNV+PSQIE  +V    ++  +Q+TL+R G 
Sbjct: 307 TDEPCACGRTHLRILRVTGRNDDMMIIRGVNVYPSQIEAALVGFAGVAPHYQLTLTRQGS 366

Query: 371 MDRLDLAVELRSEAAASVTDGERAALARELQHRIKTMVGVSSGVTVLAAGGIPATATGKA 430
           +D L +  E+      S  + +RA LAR+++H +K++VG+S  V V   G +P  + GKA
Sbjct: 367 LDHLTVEAEVED----SRGEDDRAHLARQVRHHLKSLVGISCEVIVRLPGELP-RSQGKA 421

Query: 431 RRVIDRRQAA 440
            RV D R+ A
Sbjct: 422 VRVRDLRKQA 431


Lambda     K      H
   0.319    0.136    0.400 

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: 601
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: 440
Length of database: 432
Length adjustment: 32
Effective length of query: 408
Effective length of database: 400
Effective search space:   163200
Effective search space used:   163200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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