Alignments for a candidate for mcmA in Azospirillum lipoferum B510

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Azospirillum lipoferum B510

Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate WP_012977581.1 AZL_RS27035 methylmalonyl-CoA mutase

Query= SwissProt::Q3J4D7
         (709 letters)



>NCBI__GCF_000010725.1:WP_012977581.1
          Length = 717

 Score = 1013 bits (2620), Expect = 0.0
 Identities = 519/705 (73%), Positives = 594/705 (84%), Gaps = 4/705 (0%)

Query: 8   WRKLAEKELKGKSPDS-LTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTRGVRATM 66
           W KLA K+L      S L W T EG+ VK LYT ADL GME LD LPG  PFTRG RATM
Sbjct: 12  WDKLAAKDLGADGDISKLVWKTPEGLDVKALYTAADLEGME-LDTLPGFPPFTRGPRATM 70

Query: 67  YAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRVVGDVGK 126
           YA +PWTIRQYAGFSTAE SNAFY+  L AGQ G+SVAFDLATHRGYDSDHPRVVGDVGK
Sbjct: 71  YAVKPWTIRQYAGFSTAEESNAFYKANLKAGQMGLSVAFDLATHRGYDSDHPRVVGDVGK 130

Query: 127 AGVAIDSIEDMKILFNGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAALSGTIQN 186
           AGVAIDS+EDMK+LF  IPL+K+SVSMTMNGAV+PILA +IV  EEQGV +  LSGTIQN
Sbjct: 131 AGVAIDSVEDMKVLFQDIPLDKMSVSMTMNGAVLPILAGYIVAAEEQGVSQDKLSGTIQN 190

Query: 187 DILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANLVQELAY 246
           DILKEFMVRNTYIYPPEPSMRIIADIIEYTS+ MPKFNSISISGYHMQEAGA  VQELA+
Sbjct: 191 DILKEFMVRNTYIYPPEPSMRIIADIIEYTSQHMPKFNSISISGYHMQEAGATAVQELAF 250

Query: 247 TLADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIMSE-FAP 305
           T+ADG EYVRAA+++G+ VD FA RLSFFF+IGMNFFME AKLRAARLLW  +M E F P
Sbjct: 251 TIADGLEYVRAAMSKGLPVDKFAPRLSFFFSIGMNFFMEIAKLRAARLLWSSLMQEKFQP 310

Query: 306 KKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAIALPTE 365
           K   SL LRTHCQTSGVSL EQDPYNNVIRT  EAM+A LGGTQSLHTNA DEA+ LPT+
Sbjct: 311 KDARSLALRTHCQTSGVSLTEQDPYNNVIRTTIEAMAAVLGGTQSLHTNAFDEALGLPTK 370

Query: 366 FSARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGGMTKAV 425
           FSARIARNTQ+I+ EE GVT+VVDPL GSYY+E LT  LA  A  LI  VE MGGMTKAV
Sbjct: 371 FSARIARNTQLIIAEEAGVTKVVDPLGGSYYIEHLTHSLANAALELIGRVEEMGGMTKAV 430

Query: 426 ASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQIARLE 485
            SGMPKL IEE+AARRQAAIDRGE+VIVGVNKYR    + +++LDIDN AVR+AQIARL+
Sbjct: 431 ESGMPKLLIEEAAARRQAAIDRGEEVIVGVNKYRPENPEGVDVLDIDNTAVREAQIARLK 490

Query: 486 KMRATRDEAACQAALDELTRRAAE-GGNLLEAAVDASRARASVGEISMAMEKVFGRHRAE 544
           ++RA+RDEA CQ AL  LTR AAE  GNLL  +V+A+RARA+VGEIS A+EK F RH A 
Sbjct: 491 QIRASRDEAKCQEALAALTRAAAEKTGNLLALSVEATRARATVGEISDALEKAFTRHVAV 550

Query: 545 VKTLSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVIATAFA 604
           ++++SGVYG+AYEGD+GF +IQ +V +FA EEGRRPR+LVVKMGQDGHDRGAKVIAT+FA
Sbjct: 551 IRSVSGVYGSAYEGDEGFRRIQEEVAAFAAEEGRRPRILVVKMGQDGHDRGAKVIATSFA 610

Query: 605 DIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGAGEILV 664
           DIGFDVD+G LFQTP+EAA+ A++NDVHV+G+SS AAGHKTL P+LIE L+++GAG+ILV
Sbjct: 611 DIGFDVDIGPLFQTPDEAARQAVENDVHVIGVSSQAAGHKTLVPQLIEELRKQGAGDILV 670

Query: 665 ICGGVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLIREARS 709
           +CGGVIP QDYDFL +AG  AI+GPGTNIP AA  IL ++R+ ++
Sbjct: 671 VCGGVIPPQDYDFLHKAGAAAIYGPGTNIPKAASDILGILRKQKA 715


Lambda     K      H
   0.318    0.133    0.377 

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: 1420
Number of extensions: 45
Number of successful extensions: 4
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: 709
Length of database: 717
Length adjustment: 39
Effective length of query: 670
Effective length of database: 678
Effective search space:   454260
Effective search space used:   454260
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