Alignments for a candidate for mcm-large in Calditerrivibrio nitroreducens DSM 19672

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Calditerrivibrio nitroreducens DSM 19672

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_013450693.1 CALNI_RS02840 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000183405.1:WP_013450693.1
          Length = 716

 Score =  884 bits (2284), Expect = 0.0
 Identities = 444/687 (64%), Positives = 548/687 (79%), Gaps = 6/687 (0%)

Query: 38  WETAEQIPVGTLFNEDVYKDMDW-LDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAK 96
           W TAE   V  L+  +  K++ + +DTY G+PPFV GP ATMYA +PWT+RQYAGFSTA+
Sbjct: 30  WHTAEGFDVKPLYTAEDLKNLTFDIDTYPGLPPFVRGPMATMYAGKPWTVRQYAGFSTAE 89

Query: 97  ESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGI 156
           ESNAFY+RNLAAGQ+GLSVAFDL THRGYDSD+PRV GDVG AGVAIDS+ DM+ LF GI
Sbjct: 90  ESNAFYKRNLAAGQQGLSVAFDLATHRGYDSDHPRVIGDVGKAGVAIDSVEDMKILFDGI 149

Query: 157 PLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQP 216
           PLD++SVSMTMNGAV+P++A Y+V AEEQGV  ++L+GTIQNDILKEFMVRNTYIYPP+P
Sbjct: 150 PLDKVSVSMTMNGAVIPVMAFYIVAAEEQGVSQDKLSGTIQNDILKEFMVRNTYIYPPEP 209

Query: 217 SMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLN 276
           SMRI+++I  YTS  MPK+NSISISGYH+QEAGA + +E+A+TLADG++Y+R   S GL+
Sbjct: 210 SMRIVADIIEYTSKYMPKFNSISISGYHIQEAGANSALELAFTLADGLEYVRTALSRGLD 269

Query: 277 VDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSL 336
           +D+FAPRLSFF+ IGMNFFME+AKLRAAR LWAKL+ QF PK+PKSM+LRTH QTSGWSL
Sbjct: 270 IDKFAPRLSFFFAIGMNFFMEIAKLRAARYLWAKLISQFNPKDPKSMALRTHCQTSGWSL 329

Query: 337 TAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGT 396
           TAQD YNNV+RT IEA+AA  G TQSLHTN+LDEA+ALPTDFSARIARNTQL +Q+E+  
Sbjct: 330 TAQDPYNNVIRTTIEALAAVLGGTQSLHTNALDEALALPTDFSARIARNTQLIIQEETNI 389

Query: 397 TRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQAR 456
             VIDP  GS YVE LT +L ++A   I EVE +GGM KAIE G+PK++IEE+AA+ QAR
Sbjct: 390 CNVIDPLGGSYYVENLTNELIKEAEKIIAEVEALGGMTKAIETGMPKLKIEESAAKKQAR 449

Query: 457 IDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKIT 516
           IDSG   ++GVNKY+LE E P+DVL +DN+ V   Q  KL +++ +RD + VK AL+KIT
Sbjct: 450 IDSGLDVIVGVNKYKLEKEDPIDVLMIDNTAVRNRQIQKLNEIKGKRDNKAVKEALEKIT 509

Query: 517 WAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKN 576
            AA     +  D+NLL+  ++A R  AT+GE+SDA+E VFGRY A+IR  +G Y      
Sbjct: 510 EAA-----RSNDKNLLEYAVNAARLRATLGEISDAMEAVFGRYKAEIRLQTGTYGNAYGK 564

Query: 577 TPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQT 636
              +EE RELV+EFE+ EGRRPRIL+ KMGQDGHDRG KV+ATA AD+GFDVDVGP+FQT
Sbjct: 565 KDMIEEVRELVKEFEEVEGRRPRILMVKMGQDGHDRGVKVVATALADMGFDVDVGPMFQT 624

Query: 637 PEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDEL 696
           PEE A+ A+E DVH VGVS+LA GH TLVPAL +EL K    DI++ VGGVIP QD++ L
Sbjct: 625 PEEAAKMAIENDVHAVGVSTLAAGHNTLVPALVEELKKNDGDDIVVFVGGVIPPQDYEFL 684

Query: 697 RKDGAVEIYTPGTVIPESAISLVKKLR 723
            K GA  ++ PGT I ESA  +++ +R
Sbjct: 685 YKSGASAVFGPGTNIVESAKKILECIR 711


Lambda     K      H
   0.317    0.133    0.389 

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: 1348
Number of extensions: 45
Number of successful extensions: 2
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: 728
Length of database: 716
Length adjustment: 40
Effective length of query: 688
Effective length of database: 676
Effective search space:   465088
Effective search space used:   465088
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 24 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