GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Stutzerimonas stutzeri A1501

Align Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate WP_011911348.1 PST_RS00510 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= SwissProt::Q08426
         (723 letters)



>NCBI__GCF_000013785.1:WP_011911348.1
          Length = 701

 Score =  497 bits (1279), Expect = e-145
 Identities = 294/715 (41%), Positives = 431/715 (60%), Gaps = 39/715 (5%)

Query: 11  LALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFSAGADIRGFSAPR 70
           +ALI + NPPVNA+   + + + +  ++A     + A+V+      F AGADI+ F  P 
Sbjct: 13  IALILVNNPPVNALGHAVRKGLLDAFRQADEAPEVTAVVLVCEGPTFMAGADIKEFGKPP 72

Query: 71  TFGLTLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQVGLPEVTLGLL 130
               +L  V++ I+   KP VA I G A GGGLE+ALGCHYRIA ++A+VGLPEV LGLL
Sbjct: 73  Q-APSLPEVIEVIEGCRKPSVAVIHGSALGGGLEVALGCHYRIARSDAKVGLPEVKLGLL 131

Query: 131 PGARGTQLLPRLTGVPAALDLITSGRRILADEALKLGILDKVVNSDPVEEAIRFAQRVSD 190
           PGA GTQ LPRL GV  AL++I SG+ I A EAL+  I+D++   D +E  + +A+R+ +
Sbjct: 132 PGAGGTQRLPRLAGVEKALEMIVSGQPIGAAEALEHHIVDELFEGDLIEAGLTYARRLVE 191

Query: 191 QPLESRRLCNKPIQSLPNMDSIFSEALLKMR-----RQHPGCLAQEACVRAVQAAVQYPY 245
           +    RR      +    ++ + +EAL++ +     ++ PG  +   C+ AV+AA + P 
Sbjct: 192 EGRGPRRSG----EQTRGLEGVDNEALIRAKHAEVAKRMPGLFSPLRCIAAVEAATRLPL 247

Query: 246 EVGIKKEEELFLYLLQSGQARALQYAFFAERKANKWST-PSGASWKTASARPVSSVGVVG 304
             G+K+E ELF   L S Q  AL ++FFAER+A K    PS         RP+ +  V+G
Sbjct: 248 AEGLKRERELFTECLNSPQRGALIHSFFAERQAGKIDDLPSDVK-----LRPIRTAAVIG 302

Query: 305 LGTMGRGIVISFARARIPVIAVDSDKNQLATANKMITSVLEKEASKMQQSGHPWSGPKPR 364
            GTMG GI +SFA   +PV  ++ +   L    + +    E  A+ +++        + R
Sbjct: 303 GGTMGVGIALSFANTGVPVKLLEINDEAL---QRGLQRARETYAASVKRGSLTEDAMEQR 359

Query: 365 LT--SSVKELGGV---DLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSALDVDEIA 419
           L   + V + G +   D+V+EAVFEEM +K+QVF +L AVCKP A L +NTS+LD++ IA
Sbjct: 360 LALIAGVTDYGALADADVVVEAVFEEMGVKQQVFEQLDAVCKPGAILASNTSSLDLNAIA 419

Query: 420 SSTDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVVGNCFGF 479
           + T RP  V+G HFFSPA+VM+LLEV+  + +S   +AT M + K++KK+ VVVG C GF
Sbjct: 420 AFTKRPEDVVGLHFFSPANVMRLLEVVRGERTSDEVLATAMAIGKQLKKVSVVVGVCDGF 479

Query: 480 VGNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKSRKGQGL 539
           VGNRM+  Y  +A FLLEEG+ P++VD  L  FG  MGPF + DL+GLD+G   RK Q  
Sbjct: 480 VGNRMVFQYGREAEFLLEEGATPQQVDAALRNFGMAMGPFAMRDLSGLDIGQAIRKRQRA 539

Query: 540 TGPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPDPWLSKF 599
           T P  L            +  + D LC  G  GQKTG G+Y+Y+ P  R  + +P L+  
Sbjct: 540 TLPAHLD-----------FPTVSDKLCAAGMLGQKTGAGYYRYE-PGNRTPQENPDLAPM 587

Query: 600 LSRYRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHGYGWPRH 659
           L    +   IE + + +  I+ERC+++L+NE  +IL EGIA     IDV+YL+GYG+P  
Sbjct: 588 LEAASREKGIERKALDEQYIVERCIFALVNEGAKILEEGIAQRSSDIDVIYLNGYGFPAF 647

Query: 660 KGGPMFYASTVGLPTVLEKLQKYYRQNPDIPQLEPSDYLKKLASQGNPPLKEWQS 714
           +GGPM+YA +VGL  VL ++++ + +  D    +P+  L+KLA++G     EWQ+
Sbjct: 648 RGGPMYYADSVGLDKVLARVKELHARCGD--WWKPAPLLEKLAAEGR-TFTEWQA 699


Lambda     K      H
   0.319    0.136    0.405 

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: 1171
Number of extensions: 54
Number of successful extensions: 7
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: 723
Length of database: 701
Length adjustment: 39
Effective length of query: 684
Effective length of database: 662
Effective search space:   452808
Effective search space used:   452808
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 (21.7 bits)
S2: 55 (25.8 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