Alignments for a candidate for mcmA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Cupriavidus basilensis 4G11

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate RR42_RS01600 RR42_RS01600 methylmalonyl-CoA mutase

Query= BRENDA::Q8Y2U5
         (1099 letters)



>FitnessBrowser__Cup4G11:RR42_RS01600
          Length = 1102

 Score = 1812 bits (4693), Expect = 0.0
 Identities = 920/1107 (83%), Positives = 986/1107 (89%), Gaps = 13/1107 (1%)

Query: 1    MTDLS--------AARAAEPTSASEPGAVSNKVRFVTAASLFDGHDASINIMRRILQSMG 52
            MTDLS         A+   P  A  P    NKVRFVTAASLFDGHDASINIMRRILQS G
Sbjct: 1    MTDLSDVQKGAQPGAQPGAPHQAQGPKGPVNKVRFVTAASLFDGHDASINIMRRILQSSG 60

Query: 53   CEVIHLGHNRSVDEVVNAALQEDVQGIAVSSYQGGHVEYFKYMIDALRARGGEHIQVFGG 112
            CEVIHLGHNRSV+EVV+AALQEDVQGIA+SSYQGGHVEYFKYM+D LR RGGEHIQ+FGG
Sbjct: 61   CEVIHLGHNRSVEEVVSAALQEDVQGIAISSYQGGHVEYFKYMVDLLRRRGGEHIQLFGG 120

Query: 113  GGGVIVPAEIRELQDYGVARIYSPEDGQRMGLAGMIADMVRRCDIDLAAYAPTTLEPVAK 172
            GGGVIV  EIRELQ YGVARI+SPEDGQR+GLAGMIADMV+RCDIDLA YAP TL+ +  
Sbjct: 121  GGGVIVADEIRELQAYGVARIFSPEDGQRLGLAGMIADMVQRCDIDLARYAPATLDAMKG 180

Query: 173  GDRRALAQLITALESGRIDPALRQAVHARAATAHTPVLGITGTGGAGKSSLTDELIRRFR 232
            GDRRALAQLITALE+G+ DPAL   + A AAT  TPVLGITGTGGAGKSSLTDELIRR R
Sbjct: 181  GDRRALAQLITALENGKADPALADTLRAEAATVKTPVLGITGTGGAGKSSLTDELIRRIR 240

Query: 233  LDQHDRLRIAVISIDPSRRKSGGALLGDRIRMNAINHPNLFVRSLATREASSEISDALPD 292
            LDQ D L IAVISIDPSRRKSGGALLGDRIRMNAINHP++F+RS+ATREA SEIS ALPD
Sbjct: 241  LDQRDALSIAVISIDPSRRKSGGALLGDRIRMNAINHPHIFMRSMATREAGSEISRALPD 300

Query: 293  VIAACRAGGFDLIIVETSGIGQGDAAIVPHADLSLYVMTPEFGAASQLEKIDMLDFADLV 352
            V+AAC+  GFDLIIVETSGIGQGDAAIV H DLSLYVMTPEFGAASQLEKIDMLDFAD V
Sbjct: 301  VLAACKVAGFDLIIVETSGIGQGDAAIVAHVDLSLYVMTPEFGAASQLEKIDMLDFADFV 360

Query: 353  AINKFDRKGAQDAWRDVAKQVQRNREQWHAKPEDMPVFGTQASHFNDDGVTALYHALADR 412
            AINKFDRKGAQDAWRDVAKQVQRNREQWHAKPE+MPV+GTQAS FNDDGVT LY  L + 
Sbjct: 361  AINKFDRKGAQDAWRDVAKQVQRNREQWHAKPEEMPVYGTQASRFNDDGVTMLYQGLREA 420

Query: 413  LAERGMALAERTLPRPAGTCSTSHDAIVPPARVRYLAEVADTVRGYHRRVDAQSGLARER 472
            L  RGM      LP+ +G  ST  + IVPPAR RYLAE+ADTVR YHRRVDAQS LARER
Sbjct: 421  LCARGMRAPAGVLPQLSGRVSTGQNVIVPPARNRYLAEIADTVRAYHRRVDAQSRLARER 480

Query: 473  QQLQASRRMLEAAGAAADVLTALDAQAAERDARLGAAERKLLAMWPDLRRAYAGDEYVVK 532
            QQL+ +RRML AA    D   AL A A ERDA LGA ERKLLAMWP +R+AY+GDEYVVK
Sbjct: 481  QQLREARRMLLAASGQEDQGEALQALATERDAALGAQERKLLAMWPQMRKAYSGDEYVVK 540

Query: 533  IRDRELRTPLTYTTLSGTTLRKVVLPPYEDDGEILRWLMRENVPGSFPYTAGVFAFKRRG 592
            IRD+E+RT LT TTLSGTT+RKVVLP +EDDGE+L+WL+RENVPGSFPYTAGVFAFKR  
Sbjct: 541  IRDKEIRTTLTTTTLSGTTVRKVVLPRFEDDGEVLKWLLRENVPGSFPYTAGVFAFKRE- 599

Query: 593  DVGGEDPTRMFAGEGDALRTNRRFKLVSEGMEAKRLSTAFDSVTLYGEDPDPRPDIYGKV 652
                EDPTRMFAGEGDA RTNRRFKLVSEGM+AKRLSTAFDSVTLYGEDP  RPDIYGKV
Sbjct: 600  ---NEDPTRMFAGEGDAFRTNRRFKLVSEGMDAKRLSTAFDSVTLYGEDPHTRPDIYGKV 656

Query: 653  GNAGVSIATLDDLKVLYDGFDLTSPNTSVSMTINGPAPTILAMFMNTALDQNLARFRADN 712
            GN+GVSIATLDD+KVLYDGFDLTSP+TSVSMTINGPAPTILAMFMNTA+DQ   +FRADN
Sbjct: 657  GNSGVSIATLDDMKVLYDGFDLTSPSTSVSMTINGPAPTILAMFMNTAIDQQFDKFRADN 716

Query: 713  GREPTEGEEAKIRAWVLQNVRGTVQADILKEDQGQNTCIFSTAFSLKVMGDIQEYFVHHQ 772
             REPT  E+ KIRAWVLQNVRGTVQADILKEDQGQNTCIFST FSLKVMGDIQ YFVHHQ
Sbjct: 717  DREPTVDEQGKIRAWVLQNVRGTVQADILKEDQGQNTCIFSTEFSLKVMGDIQAYFVHHQ 776

Query: 773  VRNFYSVSISGYHIAEAGANPISQLAFTLANGFTYVEAYLARGMHIDDFAPNLSFFFSNG 832
            VRNFYSVSISGYHIAEAGANPISQLAFTL+NGFTYVEAYLARGMHIDDFAPNLSFFFSNG
Sbjct: 777  VRNFYSVSISGYHIAEAGANPISQLAFTLSNGFTYVEAYLARGMHIDDFAPNLSFFFSNG 836

Query: 833  MDPEYSVLGRVARRIWAVTMRDKYGANERSQKLKYHVQTSGRSLHAQEIAFNDIRTTLQA 892
            MDPEYSVLGRVARRIWAVT+RDKYGANERSQKLKYH+QTSGRSLHAQEI FNDIRTTLQA
Sbjct: 837  MDPEYSVLGRVARRIWAVTLRDKYGANERSQKLKYHIQTSGRSLHAQEIDFNDIRTTLQA 896

Query: 893  LIAIYDNCNSLHTNAYDEAITTPTAESVRRALAIQLIINREWGLAKCENPNQGSFIIDEL 952
            LIAIYDNCNSLHTNAYDEAITTPT ESVRRALAIQLIINREWG+A+CENPNQGSF+IDEL
Sbjct: 897  LIAIYDNCNSLHTNAYDEAITTPTGESVRRALAIQLIINREWGVARCENPNQGSFLIDEL 956

Query: 953  TDLVEAAVLREFERLAERGGVLGAMETGYQRGRIQEESMLYEQRKHDGSLPIVGVNTFRN 1012
            TDLVE AV++EFER+AERGGVLGAMETGYQRG+IQ+ES+ YEQRKHDG+LPI+GVNTFRN
Sbjct: 957  TDLVEDAVMQEFERIAERGGVLGAMETGYQRGKIQDESLYYEQRKHDGTLPIIGVNTFRN 1016

Query: 1013 PEAGHAAPAHIELARSSEEEKQRQLARLADFHARHAAEAPAMLQRLQRAVIDDQNVFAVL 1072
            P+ G AAP  +ELARSSEEEKQ QLARLADFHARHA  APAMLQRL++AVID+ NVFAVL
Sbjct: 1017 PD-GDAAPPSLELARSSEEEKQGQLARLADFHARHADAAPAMLQRLRQAVIDNGNVFAVL 1075

Query: 1073 MDAVRVCSLGQITHALFEVGGQYRRNM 1099
            MDAVRVCSLGQ+THALFEVGGQYRRNM
Sbjct: 1076 MDAVRVCSLGQVTHALFEVGGQYRRNM 1102


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: 3151
Number of extensions: 120
Number of successful extensions: 3
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: 1102
Length adjustment: 46
Effective length of query: 1053
Effective length of database: 1056
Effective search space:  1111968
Effective search space used:  1111968
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