Alignments for a candidate for pccA in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Magnetospirillum magneticum AMB-1

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_011386591.1 AMB_RS21445 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= reanno::PS:Dsui_0516
         (663 letters)



>NCBI__GCF_000009985.1:WP_011386591.1
          Length = 663

 Score =  866 bits (2238), Expect = 0.0
 Identities = 437/662 (66%), Positives = 519/662 (78%), Gaps = 1/662 (0%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60
           MF KILIANRGEIACRVIKTA+KMGIKTVAVYS+ADKDAL V MADEAV IGPAAS +SY
Sbjct: 1   MFTKILIANRGEIACRVIKTAKKMGIKTVAVYSDADKDALHVSMADEAVHIGPAASAQSY 60

Query: 61  LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120
           LV DKI+ ACKQTGA+AVHPGYGFLSE  EF   L + GI FIGP  ++I  MGDKIESK
Sbjct: 61  LVIDKIVDACKQTGAQAVHPGYGFLSEKREFQEALGKAGIAFIGPDAHAIFAMGDKIESK 120

Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180
           KLA EA VNT+PGY   I   D AV+IA++IGYPVM+KASAGGGGKG+R+A+NDAEAHEG
Sbjct: 121 KLAREAGVNTVPGYLGVIKDADEAVKIAREIGYPVMLKASAGGGGKGMRLAWNDAEAHEG 180

Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240
           F+S  NEA+ SFGDDRVF+EK++ +PRHIEIQVL D  G  +YL ER+CSIQRRHQKVIE
Sbjct: 181 FTSATNEAKTSFGDDRVFVEKFIEQPRHIEIQVLADGQGTTLYLGERECSIQRRHQKVIE 240

Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300
           EAPSPF+ PE RKAMGEQA ALAR VNY+SAGTVEF+V GAT EFYFLEMNTRLQVEHPV
Sbjct: 241 EAPSPFLTPETRKAMGEQACALARIVNYKSAGTVEFIVGGATGEFYFLEMNTRLQVEHPV 300

Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360
           TE+ITGLDLVEQMIRVA GEKL +TQ DV++NGW+ME R+ AEDPFR FLPSTGRL ++Q
Sbjct: 301 TEMITGLDLVEQMIRVASGEKLSITQDDVKLNGWSMEARVYAEDPFRNFLPSTGRLTRYQ 360

Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420
           PPAE    VRVDTGVY+GGEISM+YD MIAKLI +G +R+ AIA MR AL+ + IRG+S 
Sbjct: 361 PPAE-SAHVRVDTGVYEGGEISMFYDPMIAKLITYGPTRDAAIAHMRQALDEYYIRGLSH 419

Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRA 480
           NIPF A+L    RF  G   T FIA+EY  GF A+ +P DDP +LI VAA  +RR  +R 
Sbjct: 420 NIPFLASLFSKERFVKGALTTNFIAEEYANGFHANDLPADDPTVLIAVAAAANRRIHERD 479

Query: 481 AQVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYELLSDWRQGQSLF 540
            ++SGQ PGHE K GDEWVV+ +G+ H +  +P E GY V   GE  ++ +DW+ G+ LF
Sbjct: 480 TRISGQFPGHEMKAGDEWVVVMSGQYHDITVRPAENGYAVALGGETVDVRTDWQIGEPLF 539

Query: 541 NGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDLSKFLLSP 600
               +G    +Q+ER     +L H G+R D++V++  AA++  LMP KA PD+SK+LLSP
Sbjct: 540 RANVDGRAVAVQIERVGSGLRLAHAGSRVDVLVLTPHAAKMNKLMPFKAPPDMSKYLLSP 599

Query: 601 MPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLSVDEIII 660
           MPGLL ++ V  GQEVKAGE LAV+EAMKMENILKAE+D  V K    +G SL+VD+ II
Sbjct: 600 MPGLLVKLLVEAGQEVKAGEPLAVVEAMKMENILKAERDATVAKTHAASGDSLAVDQKII 659

Query: 661 EF 662
           EF
Sbjct: 660 EF 661


Lambda     K      H
   0.319    0.135    0.391 

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: 1216
Number of extensions: 51
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: 663
Length of database: 663
Length adjustment: 38
Effective length of query: 625
Effective length of database: 625
Effective search space:   390625
Effective search space used:   390625
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 (21.7 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, or view the source code.

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