Alignments for a candidate for liuB in Saccharomonospora cyanea NA-134

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Saccharomonospora cyanea NA-134

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_005453612.1 SACCYDRAFT_RS03395 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= reanno::SB2B:6937189
         (673 letters)



>NCBI__GCF_000244975.1:WP_005453612.1
          Length = 590

 Score =  385 bits (989), Expect = e-111
 Identities = 207/429 (48%), Positives = 278/429 (64%), Gaps = 2/429 (0%)

Query: 4   KLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSYLRG 63
           K+LIANRGEIA RVIR ARD G+ +VAVY+D+DRDA H  +ADE+F L  S  A +YL  
Sbjct: 9   KVLIANRGEIAVRVIRAARDAGLASVAVYADSDRDAPHARMADEAFALHGSTAAETYLVI 68

Query: 64  ELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAKLIM 123
           + ++D+AK+ GA+++HPGYGFLSENA FA+A   +G+ ++GP   AI  +G K  A+ I 
Sbjct: 69  DKLLDVAKRSGADSVHPGYGFLSENADFAQAVLDAGLTWIGPSPQAIRDLGDKVTARHIA 128

Query: 124 EKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAAIDS 183
            +AG PLVPG      S   ++A A + G P+ IKAA+GGGG+G+++  +  E+    +S
Sbjct: 129 MRAGAPLVPGTKDPVSSAEEIVAFADEHGLPVAIKAAFGGGGRGLKVARTREEIPELFES 188

Query: 184 ARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVEEAP 243
           A REA ++FG  +  +ERYL +PRHVE QV AD  GN V +  RDCS+QRRHQK+VEEAP
Sbjct: 189 ATREAVAAFGRGECFVERYLDRPRHVEAQVLADKHGNVVVVGTRDCSLQRRHQKLVEEAP 248

Query: 244 APGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVTEMV 303
           AP L D+ R+ +  +A A  +   Y GAGTVE+L+ VD +  F+E+NTRLQVEHPV+E  
Sbjct: 249 APFLTDAQREIIHTSAKAICREAGYSGAGTVEYLVGVDGTISFLEVNTRLQVEHPVSEET 308

Query: 304 TGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLREPEP 363
           TG DLV+ Q  +A G  LP  + + +  GH+ E RI  ED    FLPA G +T L  P  
Sbjct: 309 TGIDLVREQFRIAEGGTLPFPE-DPEPRGHSIEFRINGEDAGRNFLPAPGTVTKLVLPS- 366

Query: 364 SRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHNIEFL 423
              VR+DSGV E  V+   +D M+AKLIV    R +A+ R  RAL +  V GL   + F 
Sbjct: 367 GPGVRVDSGVEEGSVVGGQFDSMLAKLIVTGADRQQAIQRARRALDEMTVEGLATVLPFH 426

Query: 424 SNIAEHPAF 432
             +    AF
Sbjct: 427 RAVLRDEAF 435



 Score = 55.1 bits (131), Expect = 9e-12
 Identities = 31/75 (41%), Positives = 45/75 (60%)

Query: 586 ETASSEDKLKAPMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEFFFA 645
           + A+S D + APM GT+V   V  G +V AG+ ++V+EAMKME  + A   G V+     
Sbjct: 515 KAAASGDAVTAPMQGTIVKVAVTEGQRVEAGELVVVLEAMKMENPVTAHKAGTVAGLTAE 574

Query: 646 PGELVSDGTLLLALE 660
            G  VS G++LL L+
Sbjct: 575 VGASVSQGSVLLELK 589


Lambda     K      H
   0.317    0.134    0.380 

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: 986
Number of extensions: 42
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 673
Length of database: 590
Length adjustment: 38
Effective length of query: 635
Effective length of database: 552
Effective search space:   350520
Effective search space used:   350520
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: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update 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