GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Klebsiella michiganensis M5al

Align citrate synthase (unknown stereospecificity) (EC 2.3.3.16) (characterized)
to candidate BWI76_RS19140 BWI76_RS19140 citrate (Si)-synthase

Query= BRENDA::P45858
         (372 letters)



>FitnessBrowser__Koxy:BWI76_RS19140
          Length = 428

 Score =  161 bits (408), Expect = 3e-44
 Identities = 116/376 (30%), Positives = 186/376 (49%), Gaps = 20/376 (5%)

Query: 7   YSPGLDGVIAAETHISYLDTQSSQILIRGYDLIELSETKSYLELVHLLLEGRLPEESEME 66
           + PG       ++ IS++DT+ S +L RGY + +L+    +LE+  +LL G  P+E+  +
Sbjct: 43  FDPGFANTAGCKSAISWIDTEKSILLHRGYPVDQLARQCDFLEVAWILLRGDAPDEASYQ 102

Query: 67  TLERKINSASSLPADHLRLLELLPEDTHPMDGLRTGLSALAG-YDRQIDDRSPSANKERA 125
             +  I   S +     R+      D+HPM  +   +  LA  Y   +D  +P      A
Sbjct: 103 DFKNTITRHSLVHEQIARMCSSFRRDSHPMALMCALVGTLAAFYHDVLDVENPEHRALAA 162

Query: 126 YQLLGKMPALTAASYRIINKKEPILPLQTLSYSANFLYMMTGKLPSS------LEEQIFD 179
            +LL KMP L A SY+   ++    P   LSY+ NFL+M+   +P+       + EQ  +
Sbjct: 163 TRLLSKMPTLAAMSYKFSIEQPAQYPRNDLSYAGNFLHMLFA-IPAEQYQLNPVIEQAMN 221

Query: 180 RSLVLYSEHEMPNSTFAARVIASTHSDLYGALTGAVASLKGNLHGGANEAVMYLLLEAKT 239
           + LVL+++H    ST   R   S+ ++L+  +   +ASL G  HGGANEA M +L E  T
Sbjct: 222 QILVLHADHGQCASTTTVRAAGSSGANLFACVAAGLASLWGPAHGGANEASMRMLEEINT 281

Query: 240 TSDFEQLLQTKLKRKEKI---MGFGHRVYMKKMDPRALMMKEALQQLCDKAG--DHRLYE 294
                  L +K KR  +    +GFG+  Y + +DPRA +++E   ++ ++ G  D  L  
Sbjct: 282 VDQIPAFL-SKAKRDPQTFRRLGFGNSRY-RHLDPRAAILRETCHRVLEELGMSDMPLQV 339

Query: 295 MCEAGERLMEK----EKGLYPNLDYYAAPVYWMLGIPIPLYTPIFFSARTSGLCAHVIEQ 350
                E  +      E GL P++D+Y A +   +G+P  ++  I    RT G  AH  E 
Sbjct: 340 AMALEEVALTDPYFVENGLSPSVDFYTAVILKAMGLPSSMFVVITAVGRTLGWVAHWNEM 399

Query: 351 H-ANNRLFRPRVSYMG 365
           H A   ++RPR  Y G
Sbjct: 400 HEAPLTIYRPRQIYTG 415


Lambda     K      H
   0.317    0.134    0.381 

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: 320
Number of extensions: 14
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: 372
Length of database: 428
Length adjustment: 31
Effective length of query: 341
Effective length of database: 397
Effective search space:   135377
Effective search space used:   135377
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: 50 (23.9 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