Alignments for a candidate for mcmA in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Dechlorosoma suillum PS

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Dsui_1105 Dsui_1105 methylmalonyl-CoA mutase family protein

Query= BRENDA::Q8Y2U5
         (1099 letters)



>FitnessBrowser__PS:Dsui_1105
          Length = 1093

 Score = 1573 bits (4073), Expect = 0.0
 Identities = 810/1105 (73%), Positives = 917/1105 (82%), Gaps = 18/1105 (1%)

Query: 1    MTDLSAARAAEPTSASEPGAVSNKVRFVTAASLFDGHDASINIMRRILQSMGCEVIHLGH 60
            MTDLS A+   P          NKVRF+TAASLFDGHDASINIMRRILQS G EVIHLGH
Sbjct: 1    MTDLSIAKKIVPYKPK------NKVRFITAASLFDGHDASINIMRRILQSTGSEVIHLGH 54

Query: 61   NRSVDEVVNAALQEDVQGIAVSSYQGGHVEYFKYMIDALRARGGEHIQVFGGGGGVIVPA 120
            NRSV ++VNAALQEDVQGIA++SYQGGHVE+FKYMID L+  GGE+I+VFGGGGGVIVP+
Sbjct: 55   NRSVGDIVNAALQEDVQGIAITSYQGGHVEFFKYMIDLLKENGGENIKVFGGGGGVIVPS 114

Query: 121  EIRELQDYGVARIYSPEDGQRMGLAGMIADMVRRCDIDLAAYAPTTLEPVA----KGDRR 176
            EI+EL +YGV RIYSPEDGQ +GL GMI D+V + D +L   AP   E V      G+RR
Sbjct: 115  EIKELHEYGVTRIYSPEDGQHLGLQGMINDVVEQSDYNLTTLAPQKPEEVMAALQSGNRR 174

Query: 177  ALAQLITALESGRIDPALR-QAVHARAATAHTPVLGITGTGGAGKSSLTDELIRRFRLDQ 235
            ALA++++ALE+G     LR Q V A A  A TP LGITGTGGAGKSSLTDEL+RRFRLDQ
Sbjct: 175  ALARIVSALENGAYPEGLRKQIVEAAALVATTPTLGITGTGGAGKSSLTDELVRRFRLDQ 234

Query: 236  HDRLRIAVISIDPSRRKSGGALLGDRIRMNAINHPNLFVRSLATREASSEISDALPDVIA 295
             D L++A+ISIDPSR+++GGALLGDRIRMNAI HPN+F+RSLATRE  SEIS ALP+VIA
Sbjct: 235  EDGLKLAIISIDPSRKRTGGALLGDRIRMNAIEHPNIFMRSLATRETGSEISAALPEVIA 294

Query: 296  ACRAGGFDLIIVETSGIGQGDAAIVPHADLSLYVMTPEFGAASQLEKIDMLDFADLVAIN 355
            AC+  GFDLIIVETSGIGQGDAAIVP  D SLYVMTPEFGAASQLEKIDMLDFAD VAIN
Sbjct: 295  ACKLSGFDLIIVETSGIGQGDAAIVPLVDASLYVMTPEFGAASQLEKIDMLDFADFVAIN 354

Query: 356  KFDRKGAQDAWRDVAKQVQRNREQWHAKPEDMPVFGTQASHFNDDGVTALYHALADRLAE 415
            KFDRKGA+DA RDV KQ QRNRE +   P++MPVFGT A+ FNDDGVTALY A+  +L E
Sbjct: 355  KFDRKGAEDALRDVRKQYQRNRELFTQSPDEMPVFGTMAARFNDDGVTALYQAILPKLVE 414

Query: 416  RGMALAERTLPRPAGTCSTSHDAIVPPARVRYLAEVADTVRGYHRRVDAQSGLARERQQL 475
             G+      LP      S+   AIVP  R RYLAE+ADT+R YH+  + Q  +ARERQ L
Sbjct: 415  FGLKAKAGKLPVVTVKESSRGRAIVPVERTRYLAEIADTLRAYHKHTEEQVKIARERQSL 474

Query: 476  QASRRMLEAAGAAADV-LTALDAQAAERDARLGAAERKLLAMWPDLRRAYAGDEYVVKIR 534
            + S+ +  +   AA   L   D   A +++ L A  +KLL MWPD  +AY+GDEYVVKIR
Sbjct: 475  RISKDLFNSYDEAAKAALPKFDELIACKESELDAKAKKLLDMWPDTVKAYSGDEYVVKIR 534

Query: 535  DRELRTPLTYTTLSGTTLRKVVLPPYEDDGEILRWLMRENVPGSFPYTAGVFAFKRRGDV 594
            D+E+RT L   +LSGT ++KVVLP + DDGE LR+LM+ENVPGSFPYTAGVFAFKR G  
Sbjct: 535  DKEIRTKLVSESLSGTKIKKVVLPRFTDDGETLRFLMKENVPGSFPYTAGVFAFKREG-- 592

Query: 595  GGEDPTRMFAGEGDALRTNRRFKLVSEGMEAKRLSTAFDSVTLYGEDPDPRPDIYGKVGN 654
              EDPTRMFAGEGDA RTNRRFK VSEGM A RLSTAFDSVTLYG DPD RPDIYGK+GN
Sbjct: 593  --EDPTRMFAGEGDAFRTNRRFKKVSEGMPAHRLSTAFDSVTLYGCDPDVRPDIYGKIGN 650

Query: 655  AGVSIATLDDLKVLYDGFDLTSPNTSVSMTINGPAPTILAMFMNTALDQNLARFRADNGR 714
            +GVSIATLDD+KVLY GFDL  P TSVSMTINGPAP ILA F NTA+DQ L +FRADNGR
Sbjct: 651  SGVSIATLDDMKVLYSGFDLVCPTTSVSMTINGPAPIILACFFNTAIDQQLDKFRADNGR 710

Query: 715  EPTEGEEAKIRAWVLQNVRGTVQADILKEDQGQNTCIFSTAFSLKVMGDIQEYFVHHQVR 774
            EPTE E  KIR WVL +VRGTVQADILKEDQGQNTCIFST F+LK+MGDIQE+FVH+QV+
Sbjct: 711  EPTEDEAEKIREWVLASVRGTVQADILKEDQGQNTCIFSTEFALKMMGDIQEFFVHNQVQ 770

Query: 775  NFYSVSISGYHIAEAGANPISQLAFTLANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMD 834
            NFYSVSISGYHIAEAGANPISQLAFTLANGFTYVE+YLARGMHIDDFAPNLSFFFSNGMD
Sbjct: 771  NFYSVSISGYHIAEAGANPISQLAFTLANGFTYVESYLARGMHIDDFAPNLSFFFSNGMD 830

Query: 835  PEYSVLGRVARRIWAVTMRDKYGANERSQKLKYHVQTSGRSLHAQEIAFNDIRTTLQALI 894
            PEYSV+GRVARRIWAV M++KYGANERSQKLKYH+QTSGRSLHAQE+ FNDIRTTLQALI
Sbjct: 831  PEYSVIGRVARRIWAVAMKNKYGANERSQKLKYHIQTSGRSLHAQEMDFNDIRTTLQALI 890

Query: 895  AIYDNCNSLHTNAYDEAITTPTAESVRRALAIQLIINREWGLAKCENPNQGSFIIDELTD 954
            AIYDNCNSLHTNAYDEAITTPT ESVRRA+AIQLIINREWG+AK ENPNQG+FIIDELTD
Sbjct: 891  AIYDNCNSLHTNAYDEAITTPTEESVRRAMAIQLIINREWGVAKNENPNQGAFIIDELTD 950

Query: 955  LVEAAVLREFERLAERGGVLGAMETGYQRGRIQEESMLYEQRKHDGSLPIVGVNTFRNPE 1014
            LVE AVL+EFE +A RGGVLGAMETGYQRG+IQEES+ YE +KHDGS PI+GVNTF NP+
Sbjct: 951  LVEEAVLKEFEAIASRGGVLGAMETGYQRGKIQEESLYYEHKKHDGSYPIIGVNTFLNPK 1010

Query: 1015 AGHAAPAHIELARSSEEEKQRQLARLADFHARHAAEAPAMLQRLQRAVIDDQNVFAVLMD 1074
               +A   IELARS+EEEKQ Q+ARL DFH R+A +APAML +L++ VI++ NVFAVL++
Sbjct: 1011 G--SAQVEIELARSTEEEKQSQIARLKDFHQRNADKAPAMLAKLKQTVIENGNVFAVLVE 1068

Query: 1075 AVRVCSLGQITHALFEVGGQYRRNM 1099
            AVRVCSLGQIT AL+EVGGQYRR+M
Sbjct: 1069 AVRVCSLGQITGALYEVGGQYRRSM 1093


Lambda     K      H
   0.320    0.134    0.388 

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: 2807
Number of extensions: 88
Number of successful extensions: 7
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: 1099
Length of database: 1093
Length adjustment: 46
Effective length of query: 1053
Effective length of database: 1047
Effective search space:  1102491
Effective search space used:  1102491
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.9 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
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