GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Marinobacter adhaerens HP15

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate GFF1257 HP15_1232 fatty acid oxidation complex subunit alpha

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



>FitnessBrowser__Marino:GFF1257
          Length = 716

 Score =  303 bits (776), Expect = 2e-86
 Identities = 219/725 (30%), Positives = 344/725 (47%), Gaps = 45/725 (6%)

Query: 1   MSEVVTRATQDQVAIVTVDSP--PVNALSAAVRRGILENVNAAVAD-PAVQAIVLVCAGR 57
           MS +      DQ+  +T+D P    N ++AA R  + E       D   ++ I++  A +
Sbjct: 1   MSAIRYELGSDQILTLTIDMPGQSANTMNAAFRDALSETAAKVKEDLDNIRGIIIASAKK 60

Query: 58  TFIAGADITEFGKPPQPPA---------LNDVIAALENSPKPTIAAIHGTALGGGLEVAL 108
           TF AG D+ E  K  +  A         L   +  LE + KP +AAI+G+ALGGGLE+AL
Sbjct: 61  TFFAGGDLKELHKVTREDARTFEDMVNGLKSHMRFLETTGKPVVAAINGSALGGGLEIAL 120

Query: 109 GCHFRVAVKE--AKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALK 166
            CH+RVA+ +   +LGLPEV LGLLPG GGTQRLPR +G E A   ++ G  +    ALK
Sbjct: 121 ACHYRVAINDDSIQLGLPEVTLGLLPGGGGTQRLPRMIGLEAAFPFLMEGKKVNPKAALK 180

Query: 167 HGLVEEVVENLVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAA------KADRSIFTNAVA 220
            G++ E+ ++  A  +    +   E  P  +   D              A       A A
Sbjct: 181 AGIINELADS--ADDMITKARAFIEANPKCQQPWDQKGFRFPGGAPHHPAMAQKLAIAPA 238

Query: 221 AMTKKARG-LEAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAERE 279
            + +K +G   AP     A      + F+ G   E   F +LV+   +K     F+ +  
Sbjct: 239 MLKQKTKGCYPAPERILSAAVEGAQVDFDNGSLIETRYFAELVIGQVAKNMTGTFWFQLN 298

Query: 280 AAKVDGV-PDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIM 338
           A K  G  P+G +     +V ++GAG MG GIA S A  GI V L +   E  ++G    
Sbjct: 299 AIKAGGSRPEGVEKETFRKVGVLGAGMMGAGIAYSTATRGIDVVLKDVSVENAEKGKSYS 358

Query: 339 QKNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDA 398
           +       +RG +  +  A  ++ I      ++++  DL+IEAVFE   +K +V    + 
Sbjct: 359 ENLLAKKVSRGRMTEEQKADILSRIKATDSSDDLEGCDLVIEAVFEDSGLKAKVTQEAEP 418

Query: 399 HAKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLT 458
                 + ASNTS + I ++A  +   ++ +G+HFFSP + M+L EI+ G KT+ + L  
Sbjct: 419 KLVANGIFASNTSTIPITQLAGASANAENFIGLHFFSPVDKMQLVEIIVGEKTSDETLAR 478

Query: 459 AVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGP 518
           +    ++I K+PVVV    GF  +R+      +   +L EG  P  ++      GMP+GP
Sbjct: 479 SFDYVQQIGKIPVVVNDSRGFFTSRVFGTFVNEGICMLGEGIHPASIENAGVLAGMPVGP 538

Query: 519 FAMGDLAGL----DIGWRSRKDRGI---------KSEIADALC-EAGRFGQKTGKGYYKY 564
            A+ D   +     I  +SRKD               + DA+  E GR G+  G G+Y+Y
Sbjct: 539 LAISDEVSMTLMQHIRDQSRKDTEAAGGTWNPHPAEAVIDAMVNEHGRKGKAAGAGFYEY 598

Query: 565 EQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARP 624
               +  +  PE+ETL  +       K R +  +E+ +R+++    E  R LEE +    
Sbjct: 599 PANGKKHL-WPELETLFVN-----AEKARTVKLQELKDRILFIQAIETVRCLEEGVLRTV 652

Query: 625 SDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAE 684
            D ++  ++G G+  + GG + + +  G++   ER SA A+ T      P  LL   A  
Sbjct: 653 EDANIGSIFGIGYAPWTGGAIQFINQYGVRAFTERASALAE-TYGERFAPPKLLQEKAET 711

Query: 685 GKTFA 689
              FA
Sbjct: 712 NTPFA 716


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: 1040
Number of extensions: 52
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 699
Length of database: 716
Length adjustment: 39
Effective length of query: 660
Effective length of database: 677
Effective search space:   446820
Effective search space used:   446820
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.

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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