Alignments for a candidate for liuB in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Marinobacter adhaerens HP15

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF1023 HP15_1002 methylcrotonyl-CoA carboxylase, alpha subunit

Query= reanno::SB2B:6937189
         (673 letters)



>FitnessBrowser__Marino:GFF1023
          Length = 664

 Score =  717 bits (1850), Expect = 0.0
 Identities = 377/672 (56%), Positives = 484/672 (72%), Gaps = 15/672 (2%)

Query: 1   MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60
           MF+K+LIANRGEIACR+I+TA  MGI+ VAVYS+AD +ARHVA+ADE+F++G +  + SY
Sbjct: 1   MFSKILIANRGEIACRIIQTAHRMGIRVVAVYSEADANARHVAMADEAFHIGPAPSSESY 60

Query: 61  LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120
           LR E II+IAKK GA+AIHPGYGFLSEN  FA +CEA+ I F+GP S AI AMGSKSAAK
Sbjct: 61  LRAEKIIEIAKKSGAQAIHPGYGFLSENTGFAESCEANNIVFIGPPSSAIAAMGSKSAAK 120

Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180
            IMEKAGVPLVPGYHGDDQS  TL AEA+K G+PLL+KA  GGGGKGMR+V +  E   A
Sbjct: 121 AIMEKAGVPLVPGYHGDDQSVETLRAEAEKCGFPLLLKAVAGGGGKGMRVVNNMGEFDDA 180

Query: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240
           + +A+REA ++FGN  +L+ERYL QPRHVE+QVF D  G  VYL++RDCS+QRRHQKV+E
Sbjct: 181 LAAAKREAQNAFGNPDMLIERYLTQPRHVEIQVFCDQDGKGVYLAERDCSVQRRHQKVLE 240

Query: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVT 300
           EAPAPGL +  RK MGEAAV AA+AI+Y GAGTVEFL DVD SFFFMEMNTRLQVEHPVT
Sbjct: 241 EAPAPGLSEETRKAMGEAAVRAAQAINYVGAGTVEFLYDVDGSFFFMEMNTRLQVEHPVT 300

Query: 301 EMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLRE 360
           EMVTGQDLV+WQL VA G  LPLEQ +++  GHA E RIYAEDP+ +FLPA+G L +L  
Sbjct: 301 EMVTGQDLVEWQLKVAWGDALPLEQSQVKTRGHALEARIYAEDPDQDFLPATGNLRYLST 360

Query: 361 PEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHNI 420
           P+ S HVR+D+GV E D IS +YDPMIAKLIVWDE+R +A+ R+ +AL  YR+ G+K NI
Sbjct: 361 PDESAHVRVDTGVTEGDDISIHYDPMIAKLIVWDETRDQAINRMVQALEHYRIAGVKTNI 420

Query: 421 EFLSNIAEHPAFAQANFSTDFIGRYGDALIGDSRDEADTAFVLA---VLTQLRLREAVSQ 477
            FL  +A+   F +A  +T FI  + + L   S+ +   A VLA   VL Q + RE VS 
Sbjct: 421 RFLHALADAQPFREAELTTGFIDDHRELLFPKSKLDTHKALVLAAGFVLEQRKSREVVST 480

Query: 478 DVAGHDPFSPWSSLKGFRLSSPRRHSVTLLDDAHQSRSAELTESNGRYQLCLNDKLIELS 537
                DP+SP+     +R++S     +  L    +    ++ E + RYQ+ + D +  L+
Sbjct: 481 -----DPWSPFGRQNSWRMNSEFAQPLQ-LQVGEEIHDLKVLERDDRYQVFVGDSVYNLT 534

Query: 538 GSIEDSELKCEINGHKMKVTVSLEDGGLTVFLSSGSYH---FREVLGQVLEETASSEDKL 594
             ++D  L+  INGH++ +  +L +  L +F    +++   ++E  G   EE A SE  L
Sbjct: 535 ARLDDDYLQAVINGHRISIHGNLHNDQLMLFYEGDTFNCTVYKESYG--FEEMA-SEGSL 591

Query: 595 KAPMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEFFFAPGELVSDGT 654
            APMNG +V      GDKV+AGQ L++MEAMKME+ I+AP DGVV+E FFA G+ VS+G 
Sbjct: 592 AAPMNGAIVAVQAKVGDKVTAGQSLVIMEAMKMEHAIKAPADGVVTEIFFAEGDQVSEGA 651

Query: 655 LLLALEMADAAA 666
            L+A+E+ +  A
Sbjct: 652 ELIAIEVNEEEA 663


Lambda     K      H
   0.317    0.134    0.380 

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: 1139
Number of extensions: 58
Number of successful extensions: 5
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: 673
Length of database: 664
Length adjustment: 38
Effective length of query: 635
Effective length of database: 626
Effective search space:   397510
Effective search space used:   397510
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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

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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:

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
the source code
instructions for running GapMind on your computer

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