GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Stutzerimonas stutzeri A1501

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_011911348.1 PST_RS00510 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= metacyc::MONOMER-20678
         (699 letters)



>NCBI__GCF_000013785.1:WP_011911348.1
          Length = 701

 Score =  684 bits (1765), Expect = 0.0
 Identities = 355/696 (51%), Positives = 484/696 (69%), Gaps = 10/696 (1%)

Query: 1   MSEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60
           M++V+    +  +A++ V++PPVNAL  AVR+G+L+    A   P V A+VLVC G TF+
Sbjct: 1   MTDVIRLERRGDIALILVNNPPVNALGHAVRKGLLDAFRQADEAPEVTAVVLVCEGPTFM 60

Query: 61  AGADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120
           AGADI EFGKPPQ P+L +VI  +E   KP++A IHG+ALGGGLEVALGCH+R+A  +AK
Sbjct: 61  AGADIKEFGKPPQAPSLPEVIEVIEGCRKPSVAVIHGSALGGGLEVALGCHYRIARSDAK 120

Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVA 179
           +GLPEVKLGLLPGAGGTQRLPR  G E A++MIV G PIGAAEAL+H +V+E+ E +L+ 
Sbjct: 121 VGLPEVKLGLLPGAGGTQRLPRLAGVEKALEMIVSGQPIGAAEALEHHIVDELFEGDLIE 180

Query: 180 GAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAI 239
             + +A++++ E R  RR  +    L     + ++     A + K+  GL +P  C  A+
Sbjct: 181 AGLTYARRLVEEGRGPRRSGEQTRGLEGVD-NEALIRAKHAEVAKRMPGLFSPLRCIAAV 239

Query: 240 GAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVA 299
            AA  LP  EGLK+ERE F + + S Q  A  ++FFAER+A K+D +P   K RP+   A
Sbjct: 240 EAATRLPLAEGLKRERELFTECLNSPQRGALIHSFFAERQAGKIDDLPSDVKLRPIRTAA 299

Query: 300 IIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKR 359
           +IG GTMG GIA+SFAN G+PV L+E  +E L+RGL   ++ + A+  RG L  DA  +R
Sbjct: 300 VIGGGTMGVGIALSFANTGVPVKLLEINDEALQRGLQRARETYAASVKRGSLTEDAMEQR 359

Query: 360 MALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIA 419
           +ALI G+     + DAD+++EAVFE M VK++VF  +DA  KPGA+LASNTS L ++ IA
Sbjct: 360 LALIAGVTDYGALADADVVVEAVFEEMGVKQQVFEQLDAVCKPGAILASNTSSLDLNAIA 419

Query: 420 ATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGF 479
           A TKRP+DV+G+HFFSPANVM+L E+VRG +T+ + L TA++I K++ KV VVVGVCDGF
Sbjct: 420 AFTKRPEDVVGLHFFSPANVMRLLEVVRGERTSDEVLATAMAIGKQLKKVSVVVGVCDGF 479

Query: 480 VGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGI 539
           VGNRM+    +++E LL EGA PQQVDA +  FGM MGPFAM DL+GLDIG   RK +  
Sbjct: 480 VGNRMVFQYGREAEFLLEEGATPQQVDAALRNFGMAMGPFAMRDLSGLDIGQAIRKRQRA 539

Query: 540 K-------SEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKR 592
                     ++D LC AG  GQKTG GYY+YE G+R P  +P++  ++     + G++R
Sbjct: 540 TLPAHLDFPTVSDKLCAAGMLGQKTGAGYYRYEPGNRTPQENPDLAPMLEAASREKGIER 599

Query: 593 RDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVG 652
           + + ++ I+ER ++ ++NEGA+ILEE IA R SDIDV++L GYG+P +RGGPM+YADSVG
Sbjct: 600 KALDEQYIVERCIFALVNEGAKILEEGIAQRSSDIDVIYLNGYGFPAFRGGPMYYADSVG 659

Query: 653 LKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688
           L  +  R+        D   +PAPLL +LAAEG+TF
Sbjct: 660 LDKVLARVKELHARCGD-WWKPAPLLEKLAAEGRTF 694


Lambda     K      H
   0.317    0.134    0.383 

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: 1234
Number of extensions: 64
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: 699
Length of database: 701
Length adjustment: 39
Effective length of query: 660
Effective length of database: 662
Effective search space:   436920
Effective search space used:   436920
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: 54 (25.4 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