GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Thiothrix lacustris DSM 21227

Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_028489631.1 Q394_RS0112845 AMP-binding protein

Query= BRENDA::O74725
         (578 letters)



>NCBI__GCF_000621325.1:WP_028489631.1
          Length = 555

 Score =  171 bits (433), Expect = 7e-47
 Identities = 155/529 (29%), Positives = 244/529 (46%), Gaps = 47/529 (8%)

Query: 58  NRVDSLARSLSKEFGWAPNEGSEWDKTLAVFALNTIDSLPLFWAVHRLGGVLTPANASYS 117
           N VD L R  +         G +  + +A+   N +      +   R G V+   N  Y+
Sbjct: 52  NDVDELTRQFAAYL--IHGAGLKPGERIALMMPNLLQYPIALFGALRAGLVVVNTNPLYT 109

Query: 118 AAELTHQLLDSKAKALVTC-------------VPLLSI-SLEAAAKAGLPKNRIYLLDVP 163
             EL HQL DS A A+V               VP+ +I + E     G PK+ +  L V 
Sbjct: 110 DRELEHQLKDSGATAIVITANFAHTLQDVLDKVPIKTIITTEIGDLFGFPKSLLVNLVVK 169

Query: 164 --EQLLGGVKPPAGYKSVSELTQAGKSLPPVDELRWSAGEGARRTAFVCYSSGTSGLPKG 221
             ++++   K P   K    LT   +      +    A  G    AF+ Y+ GT+G+ KG
Sbjct: 170 YVKKMVPAFKLPTAIKFNQALTLGKQYATRFQD----AEPGHEDIAFLQYTGGTTGIAKG 225

Query: 222 VMISHRNVIANTLQIKAFEQNYRDGGGTKPASTEVALGLLPQSHIYALVVIGHAGAYRGD 281
             ++HRN+IAN LQ +A+            A  E+ +  LP  H++AL          G 
Sbjct: 226 AALTHRNIIANMLQAEAWTT------ADLVAGKEIVITALPLYHVFALTANAMFALKMGA 279

Query: 282 QTIVLPK-FELKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCSKYDLSSVTSLFTGAAP 340
           + +++    +L +++  +     + +  V  +   +L   D+  K D S +  +  G   
Sbjct: 280 KNVLITNPRDLPAFIKDLAHEPFTFITGVNTLYNALLNHPDI-GKVDFSRL-KISLGGGM 337

Query: 341 LGMETAADFLKLYPNILIRQGYGLTETCTVVSSTHPHDI--WLGSSGALLPGVEARIVTP 398
              ++ A+  K    + + + YGLTET   V+  +P D+  + G  G  +P  E  I   
Sbjct: 338 AVQKSVAERWKALTGVTLLEAYGLTETSPAVA-INPVDLHDYNGMIGLPVPSTEVSIRDV 396

Query: 399 ENKEITTYDSPGELVVRSPSVVLGYLNNEKATAETFV-DGWMRTGDEAVIRRSPKGIEHV 457
           +  E+    + GEL VR P V+ GY      TA   V DGW+RTGD AVI      +  +
Sbjct: 397 DGNELDI-GAAGELWVRGPQVMQGYWQRPDETANVMVEDGWLRTGDVAVINE----LGFI 451

Query: 458 FIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDRAGEVPKAIVVKSASAG 517
            +VDR+K+++ V G  V P E+E  + +HP V +  VI  PD+ +GE+ KA VVK     
Sbjct: 452 KLVDRLKDMVLVSGFNVYPNEVEDVLASHPKVLEAGVIGAPDEHSGEIVKAFVVK----- 506

Query: 518 SDESVS-QALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRRLIRD 565
            DES++ + L  Y     + +K  K  I FV ++PKS  GKILR+ +RD
Sbjct: 507 KDESLTLEELRAYCRYELSAYKCPK-QIVFVTSLPKSNVGKILRKELRD 554


Lambda     K      H
   0.316    0.134    0.392 

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: 709
Number of extensions: 32
Number of successful extensions: 6
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: 578
Length of database: 555
Length adjustment: 36
Effective length of query: 542
Effective length of database: 519
Effective search space:   281298
Effective search space used:   281298
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. 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