GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Klebsiella michiganensis M5al

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate BWI76_RS02995 BWI76_RS02995 aspartate carbamoyltransferase

Query= curated2:P18186
         (319 letters)



>FitnessBrowser__Koxy:BWI76_RS02995
          Length = 311

 Score =  136 bits (343), Expect = 6e-37
 Identities = 106/316 (33%), Positives = 164/316 (51%), Gaps = 29/316 (9%)

Query: 9   LYGKDLLTLKDLSEEDINALLAEAGELKQNKIQPIFHGKTLAMIFEKSSTRTRVSFEAGM 68
           LY K ++++ DLS ED+  +LA A +LK +    +   K +A  F ++STRTR+SFE  M
Sbjct: 5   LYQKHIISINDLSREDLELVLATAAKLKAHPQPELLKHKVIASCFFEASTRTRLSFETSM 64

Query: 69  AQLGGSAL-FLSQKDLQLG-RGETVADTAKVLSGYVDAIMIRTFEHEKVEELAKE--ADI 124
            +LG S + F    +  LG +GET+ADT  V+S YVDAI++R    E    LA E    I
Sbjct: 65  HRLGASVVGFSDSSNTSLGKKGETLADTISVISTYVDAIVMR-HPQEGAARLATEFSGGI 123

Query: 125 PVIN-GLTDKYHPCQALADLLTIKEIKGKLKGVKVAYIGD--GNNVAHSLMIGCAKMG-- 179
           PV+N G     HP Q L DL TI+E +G+L+ + VA +GD       HSL    AK    
Sbjct: 124 PVLNAGDGANQHPTQTLLDLFTIQETQGRLENLNVAMVGDLKYGRTVHSLTQALAKFNGN 183

Query: 180 -----CDISIASPKGYEVLDEAAEAAKTYALQSGSSVTLTDDPIEAVKDADVIYSDVFTS 234
                   ++A P+   +LD   +    ++L S           E +++ D++Y  +   
Sbjct: 184 RFYFIAPDALAMPQ--YILDMLDDKGIAWSLHSAIE--------EVMEEVDILY--MTRV 231

Query: 235 MGQEAEEQERLAVFAPYQVNAALVSHAKPDYTFLHCLPAHREEEVTAEIIDGPNSAVFQQ 294
             +  +  E   V A + + AA +  A+ +   LH LP  R +E+T ++   P++  FQQ
Sbjct: 232 QKERLDPSEYANVKAQFVLRAADLEGARANMKVLHPLP--RIDEITTDVDKTPHAWYFQQ 289

Query: 295 AENRLHVQKALLKAIL 310
           A N +  ++ALL  +L
Sbjct: 290 AGNGIFARQALLALVL 305


Lambda     K      H
   0.315    0.131    0.361 

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: 201
Number of extensions: 20
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: 319
Length of database: 311
Length adjustment: 27
Effective length of query: 292
Effective length of database: 284
Effective search space:    82928
Effective search space used:    82928
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 (21.5 bits)
S2: 48 (23.1 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