GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Pseudomonas stutzeri RCH2

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate GFF2604 Psest_2654 fatty oxidation complex, alpha subunit FadB

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



>FitnessBrowser__psRCH2:GFF2604
          Length = 715

 Score =  352 bits (902), Expect = e-101
 Identities = 226/689 (32%), Positives = 349/689 (50%), Gaps = 27/689 (3%)

Query: 23  VNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFGKPPQPP------- 75
           VN  +      + + V+A  AD +V+ +++      FI GADITEF    +         
Sbjct: 29  VNKFNRLTLNDLRQAVDAIKADASVKGVIVTSGKDVFIVGADITEFVDNFKMADEELVAG 88

Query: 76  --ALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLPG 133
               N + +  E+   PT+AAI+G ALGGG E+ +   +RV    AK+GLPEVKLG+ PG
Sbjct: 89  NLEANKIFSDFEDLGVPTVAAINGIALGGGFEMCMAADYRVMSTTAKVGLPEVKLGIYPG 148

Query: 134 AGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENLVAGAVAFAKKVLA- 190
            GGT RLPR +G + AV+ I  G    A +ALK   V+ VV  + L A A+   K+ ++ 
Sbjct: 149 FGGTVRLPRLIGVDNAVEWIASGKENRAEDALKVHAVDAVVAPDKLQAAALDLVKRAISG 208

Query: 191 --EKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLPFE 248
             + +  R+ + D  KL A +   +  T+      +      AP      I  A +   +
Sbjct: 209 ELDYKAKRQPKLDKLKLNAIEQMMAFETSKAFVAGQAGPNYPAPVEAIKTIQKAANFTRD 268

Query: 249 EGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGG 308
           + ++ E  GF+KL  +  +++    F +++E  K     D  + R V   A++GAG MGG
Sbjct: 269 KAIEVEAAGFVKLAKTSVAQSLVGLFLSDQELKKKAKAYD-KQARDVKLAAVLGAGIMGG 327

Query: 309 GIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVG 368
           GIA   A  G P+ + +  EE ++ GL    K       +G L  D  A+ +  I   + 
Sbjct: 328 GIAYQSAVKGTPILMKDIREEGIQMGLDEASKLLGKRVEKGRLTADKMAQALNAIRPTMS 387

Query: 369 LENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDV 428
             +  + D+++EAV E   VK  V   V+ H +  A++ASNTS +SI+ +A   KRP++ 
Sbjct: 388 YGDFGNVDIVVEAVVENPKVKHAVLAEVEGHVREDAIIASNTSTISINYLAQALKRPENF 447

Query: 429 LGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAAR 488
            GMHFF+P ++M L E++RG KT+  A+ T V+ AKK+ K PVVV  C GF+ NR+L   
Sbjct: 448 CGMHFFNPVHMMPLVEVIRGEKTSEVAIATTVAYAKKMGKSPVVVNDCPGFLVNRVLFPY 507

Query: 489 SKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR---------KDRGI 539
                + +  G    + D V+ KFG PMGP  + D+ G+D G   R         + +  
Sbjct: 508 FGGFARAIAHGVDFVRADKVMEKFGWPMGPAYLMDVVGMDTGHHGRDVMAEGFPDRMKDD 567

Query: 540 KSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEE 599
                D + EA R GQK GKG+Y YE   +   P   V+    + L  +  + R+++DE+
Sbjct: 568 TRTAVDVMYEANRLGQKNGKGFYAYEMDKKG-KPKKVVDAQAYELLKPIVAETRELSDED 626

Query: 600 ILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAER 659
           I+  M+ P+  E  R LE+ I    ++ D+  +YG G+P +RGG + Y DS+G+      
Sbjct: 627 IINYMMIPLCLETVRCLEDGIVETAAEADMGLIYGIGFPPFRGGALRYIDSIGVAEFVAM 686

Query: 660 LSAYAKATNDPSLEPAPLLARLAAEGKTF 688
              YA     P   P   L  +AA G+ F
Sbjct: 687 ADKYADL--GPLYHPTAKLREMAANGQRF 713


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: 967
Number of extensions: 52
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: 699
Length of database: 715
Length adjustment: 39
Effective length of query: 660
Effective length of database: 676
Effective search space:   446160
Effective search space used:   446160
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: 55 (25.8 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