GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Azospirillum thiophilum BV-S

Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate WP_045584011.1 AL072_RS25820 acetyl-CoA carboxylase biotin carboxylase subunit

Query= BRENDA::Q9I299
         (655 letters)



>NCBI__GCF_001305595.1:WP_045584011.1
          Length = 454

 Score =  438 bits (1126), Expect = e-127
 Identities = 230/442 (52%), Positives = 305/442 (69%), Gaps = 3/442 (0%)

Query: 8   IQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYL 67
           ++R+LVANRGEIA RV+R+ R LGI +V VHS  D+ +  V  AD +V +GG    +SYL
Sbjct: 1   MRRILVANRGEIALRVIRACRDLGIEAVQVHSSADQDSLPVRLADASVCIGGPSATESYL 60

Query: 68  RGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKA 127
             D +I AA+ +G  A+HPGYGFLSENA FAR CEE GL+F+GP  A IDAMG K+AA+ 
Sbjct: 61  NVDALIDAAMRTGCDAVHPGYGFLSENAGFARTCEERGLVFIGPNPAVIDAMGDKAAARR 120

Query: 128 LMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEAL 187
           +  EAGVP+ PG        +     AG++GYPVL+KA+AGGGG+GM+VV  EA L + L
Sbjct: 121 IAVEAGVPVSPGSPDPVSGADEAAAIAGKVGYPVLIKASAGGGGRGMRVVADEAALRDTL 180

Query: 188 SSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEE 247
             A  EA A+FG+  + +EKYL + RHVE+QV  D   H +++ ERDCS+QRRHQK+VEE
Sbjct: 181 ERASAEAAASFGNGAVYIEKYLPRVRHVEVQVMGD-GDHVVHMGERDCSVQRRHQKLVEE 239

Query: 248 APAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLD-ERGQFFFMEMNTRLQVEHPVT 306
           +P+PG+ ++LRR + E+A   A+ + Y  AGT+EF++D +  +FFF+EMNTR+QVEHPVT
Sbjct: 240 SPSPGISSDLRRRITESACALARHVRYRSAGTLEFIVDADSEEFFFIEMNTRIQVEHPVT 299

Query: 307 EAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYRE 366
           EA+TGLDLV  QI VA    LPL QE V  +GHAIE R+ AEDP+  FLP  G L  +  
Sbjct: 300 EAVTGLDLVKLQIIVADTGILPLRQEDVHFSGHAIECRINAEDPDKGFLPKPGVLKDF-H 358

Query: 367 AAAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNL 426
           A AGPG RVDS    G  + P+YD +LAK+++WG TREEA  R+   LAET V G+ T +
Sbjct: 359 APAGPGIRVDSHAYPGYALPPYYDSLLAKIVSWGRTREEAIARMRRALAETRVEGVPTTI 418

Query: 427 AFLRRILGHPAFAAAELDTGFI 448
            F +R+L    F A  + T ++
Sbjct: 419 GFHQRLLSDDRFLAGAVHTRYV 440


Lambda     K      H
   0.319    0.135    0.397 

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: 775
Number of extensions: 31
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: 655
Length of database: 454
Length adjustment: 35
Effective length of query: 620
Effective length of database: 419
Effective search space:   259780
Effective search space used:   259780
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 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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