GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Rhodanobacter denitrificans FW104-10B01

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_027490801.1 LRK54_RS04500 acetyl ornithine aminotransferase family protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>NCBI__GCF_021560695.1:WP_027490801.1
          Length = 444

 Score =  248 bits (634), Expect = 2e-70
 Identities = 156/411 (37%), Positives = 212/411 (51%), Gaps = 40/411 (9%)

Query: 15  QVMVPNYA-PAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANK 73
           +V+ P+Y     F+   G G+ VWD  G   +DF  GIAV   GHAHP +V A+ + A K
Sbjct: 28  EVISPSYPRDYPFVMSHGRGTEVWDVDGNRFLDFMAGIAVCATGHAHPQVVKAVQDAAAK 87

Query: 74  LWHVSNVFTNEPALRLAHKLVDAT---FAERVFFCNSGAEANEAAFKLARRVAHDRFGTE 130
             H+S+ + +E    L  +L            F C SG EA E A KLAR V      T 
Sbjct: 88  FLHISSDYWHEEMTGLGERLAAVAPLGAPAMSFICQSGTEAVEGALKLARYV------TG 141

Query: 131 KYEIVAALNSFHGRTLFTVNVGGQSKYSD--GFGPKITGITHVPY-NDLAAL------KA 181
           +   +  L  FHGRT  +++    SKY+   GF P + G+THVPY N    L       A
Sbjct: 142 RPRFIGFLGGFHGRTFGSLSFTS-SKYTQQKGFSPTLAGVTHVPYPNPYRPLFAGDDQGA 200

Query: 182 AVSD-------------KTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEV 228
           AV D             +  A+++EP+QGEGG L     +L G R LCD H  LL+FDEV
Sbjct: 201 AVLDYIRMLFQRSVPPSEVAAILIEPMQGEGGYLTPPDGFLAGLRALCDEHGILLIFDEV 260

Query: 229 QTGMGRSGKLFAYQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGN 288
           Q+G+GR+G++FA +H+GV PDI+TSAK LG G PI A++  + +      G HG TYGGN
Sbjct: 261 QSGIGRTGRMFACEHWGVQPDIITSAKGLGSGLPIGAVIAKKSIMSQWKRGAHGNTYGGN 320

Query: 289 PLACAVAEAVIDVINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVL-- 346
           P+ CA A A +D++    + N      D F  RL ++   Y    EVRG GL +G  L  
Sbjct: 321 PVTCAAANATLDLVRGGLMDNAARV-GDHFMARLRELQRDYPCIGEVRGKGLWIGMELIE 379

Query: 347 SDAWKGKAKDIFNA----AEREGLMILQAGPDVIRFAPSLVVEDADIDAGL 393
            D  K  A  +  A    A   GL++L  G   +RF P L V   ++D  +
Sbjct: 380 DDGKKTPATALCEAVVQRAFHNGLLLLSCGTSTVRFMPPLNVSVGEVDEAI 430


Lambda     K      H
   0.320    0.136    0.400 

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: 444
Number of extensions: 25
Number of successful extensions: 7
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: 406
Length of database: 444
Length adjustment: 32
Effective length of query: 374
Effective length of database: 412
Effective search space:   154088
Effective search space used:   154088
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: 51 (24.3 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:

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