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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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:

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:

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:

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:

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