Aligments for a candidate for pimF in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__Marino:GFF1257 HP15_1232 fatty acid oxidation
           complex subunit alpha
          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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources