Alignments for a candidate for liuB in Thauera aminoaromatica S2

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Thauera aminoaromatica S2

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_004314673.1 C665_RS13545 acetyl-CoA carboxylase biotin carboxylase subunit

Query= reanno::pseudo5_N2C3_1:AO356_01595
         (649 letters)



>NCBI__GCF_000310185.1:WP_004314673.1
          Length = 662

 Score =  507 bits (1306), Expect = e-148
 Identities = 296/668 (44%), Positives = 408/668 (61%), Gaps = 38/668 (5%)

Query: 9   LLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68
           +L+ANRGEI CRV++TAR MG+ TVAV+S  D++A H   AD  V +G + + +SYL +D
Sbjct: 5   ILIANRGEITCRVIKTARKMGIKTVAVYSEADKNALHVELADEAVCIGPAASKESYLVMD 64

Query: 69  KLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKTLME 128
           K+IAA K +GA+A+HPGYGFLSENA F+R +E  G+ F+GP   ++  MG K  +K L  
Sbjct: 65  KIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSVAKMGDKIESKKLAI 124

Query: 129 TAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188
            AGV  +PGY+      +   + A++IGYPV++KA+AGGGGKG++V  +  +  E  AS 
Sbjct: 125 AAGVNTIPGYNDAISGPDEAVEIAKKIGYPVMIKASAGGGGKGLRVAFNDKEAHEGFASC 184

Query: 189 QREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248
             EA+++FGD R+ +EKY+L+PRH+EIQV  D HGN +YLNERDCSIQRRHQKV+EEAP+
Sbjct: 185 VNEARNAFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEEAPS 244

Query: 249 PGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLD-ARGEFFFMEMNTRLQVEHPVTEAI 307
           P + P +R+AMGE AV  A+A+ Y  AGTVEF++  A  EF+F+EMNTRLQVEHPVTE I
Sbjct: 245 PFVDPAMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVTELI 304

Query: 308 TGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLALYRESAE 367
           TGLDLV   IRVA GE LP+ QA V + G A+E R+ AEDP   FLP+TGRL  ++  AE
Sbjct: 305 TGLDLVEQMIRVAYGEKLPLAQADVKIDGWAMECRINAEDPFRGFLPSTGRLIKFQPPAE 364

Query: 368 GPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGLKTNIGFL 427
           G G RVD+GV EG EIS FYD M+ KLI  G+DR+ A  R+   L+ FVI G+ +NI F 
Sbjct: 365 GNGVRVDTGVYEGGEISMFYDSMIAKLIVHGKDRQDAIERMRDALNGFVIRGISSNIPFQ 424

Query: 428 RRIVAHPAFAAAELDTGFIPR-----YQAQLLPEPSELDDAFWFAAAQGVA----LSLAP 478
             ++ HP F +   +TGFI       + A ++P     DD    AA    A    +  A 
Sbjct: 425 AALLQHPRFCSGHFNTGFIAEEYPKGFDASMVPH----DDPALLAAVATFARMRYIERAV 480

Query: 479 HVRGDDAG------SPWASTTGMRLGLPR----ETTLHLSCEGQDRALTLD------VTA 522
            + G  AG      S W    G +    R    E  L ++CEG+   +  D      + A
Sbjct: 481 QIEGQLAGHGRKVASEWVVVMGGKQYAMRTAAIEGGLAVTCEGRTYNIVSDWKFGELLFA 540

Query: 523 HCAELEGERLTIEHHGVRR--SHRAIRQVDSLYLQWEGDLHRIDLYDPLAAAEASHSHQG 580
                    L IE  G+R   SH  + QV+ + +      H + L       + S     
Sbjct: 541 GTVNGAPIGLQIERRGLRYRISHFGL-QVEPVVMTVRA-AHLLSLMPAKLPPDLSKF--- 595

Query: 581 GLVAPMNGSIVRVLVGVGQTVEAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSE 640
            L++PM G +  + V  GQ V+AG +L ++EAMKME+ ++A + G +K +  + G  +S 
Sbjct: 596 -LLSPMPGLLREIAVTEGQDVKAGEKLAIIEAMKMENVLKAEQDGKVKKIVAKPGASLSV 654

Query: 641 GSALVAFE 648
              ++ FE
Sbjct: 655 DEVIIEFE 662


Lambda     K      H
   0.319    0.134    0.390 

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: 1010
Number of extensions: 59
Number of successful extensions: 3
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: 649
Length of database: 662
Length adjustment: 38
Effective length of query: 611
Effective length of database: 624
Effective search space:   381264
Effective search space used:   381264
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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