GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|NCBI__GCF_000009985.1:WP_011383657.1 AMB_RS06320
           phenylacetate--CoA ligase
          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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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