Alignments for a candidate for uxaA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxaA in Klebsiella michiganensis M5al

Align Altronate dehydratase (EC 4.2.1.7) (characterized)
to candidate BWI76_RS26325 BWI76_RS26325 altronate hydrolase

Query= reanno::Pedo557:CA265_RS19875
         (548 letters)



>FitnessBrowser__Koxy:BWI76_RS26325
          Length = 531

 Score =  518 bits (1335), Expect = e-151
 Identities = 268/545 (49%), Positives = 352/545 (64%), Gaps = 18/545 (3%)

Query: 5   ILKIHPNDNVLVALQNLAKGETVIYDGHEYILQDDIQAKHKFFMQDMNAGDHIIMYGVLV 64
           ILKI P DN++VALQ+L K + V ++   Y+L+ D++AKHKF  +D+  GD + +YGV V
Sbjct: 4   ILKIDPTDNLIVALQDLRKEQQVNWNDEAYVLRSDVKAKHKFATEDIAPGDIVSLYGVPV 63

Query: 65  GKAQHFILKGGLMDTENTKHASDPYEFRPYH-YEWHAPDVSKFEGRTFNGYIRSDGRVGT 123
           GKA   I +G  + T+N KH + P        Y+W  PDV  ++ RTF G +R DGRV T
Sbjct: 64  GKATRPIARGEAITTDNIKHYAAPVSLNDVAPYDWQQPDVFAWQQRTFKGIVREDGRVAT 123

Query: 124 ANYWLFIPTVFCENRNLDVIREALHNELGYAVTDKYKSYAHQLVEAYKNGEILAEADPSS 183
           ANYWL IP VFCENRN+  + +AL++ LGYA  +  K++A Q+  A              
Sbjct: 124 ANYWLVIPLVFCENRNVQRVTDALNDALGYA-NNGLKNFARQVTSA-------------- 168

Query: 184 IGLANPSANRVFKNVDGIKFLNHQGGCGGTRQDAAVLSKLLAAYADHPNVAGVTVLSLGC 243
            G  N + +  F ++DGI+ +    GCGG   D+  +  +LAAY+DHPNV GVTV +LGC
Sbjct: 169 -GALNDTRHLPFPHLDGIRCITVNSGCGGATSDSMTMCDVLAAYSDHPNVLGVTVFALGC 227

Query: 244 QNLQVKDFMDDLKHRSPNFDKPLFVFEQQQSQSEEQLVKEAIRKTFIGLTEINKIERQPA 303
           +  ++ DF   L  R+PNF KP+  F QQ   SEE+++++A+ +T+  + E    ERQ  
Sbjct: 228 EKARIVDFKAALAKRNPNFSKPIIYFRQQDWSSEEKMMQDALTETYNAIREAPVAERQNV 287

Query: 304 PLSKLVLGVKCGGSDGFSGISANPAVGYTSDLLVALGGTVLLAEFPELCGAEQQLIDRTK 363
           PLS+L +GVKCG SDGFSGISANPA+G  SD LVALGG   LAEFPELCGAE  ++ R  
Sbjct: 288 PLSRLKIGVKCGASDGFSGISANPAMGEVSDRLVALGGASGLAEFPELCGAEGDIVQRCT 347

Query: 364 DETAARKFIQLMTAYNQSAENVGSGFFMNPSPGNIKDGLITDAIKSTGAAKKGGTSPVED 423
                 KF+ LM  Y   A   G+    NPSPGNI DGLITDAIKS GAAKKGG +PV  
Sbjct: 348 TRELKEKFLSLMKNYEHVANFFGTTIADNPSPGNIADGLITDAIKSAGAAKKGGRAPVSA 407

Query: 424 VLDYTEPATKPGLNLVCTPGNDVEATTGKAASGATLILFTTGLGTPTGNPVCPTIKVSTN 483
           V DY EP  + GL+LVCTPGNDV+A TG  A+G  +++F+TGLGTPTGNP+ P +KVSTN
Sbjct: 408 VCDYAEPMGESGLSLVCTPGNDVDAVTGLVAAGCNVVIFSTGLGTPTGNPIVPVLKVSTN 467

Query: 484 NALTKRMGDIIDINCGPVIEGEKTIEQMGEDILEYCIKAASGEVIPKAVLLNQDDFIPWK 543
           +AL K+M DIID +CGP+IEG   +  + + + E  I  ASG    KA  L Q DF+ WK
Sbjct: 468 SALAKKMPDIIDYDCGPIIEG-TPLADIADGLFEKIIATASGTWRTKADALEQYDFMLWK 526

Query: 544 RGVSL 548
           R + L
Sbjct: 527 RSLEL 531


Lambda     K      H
   0.317    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: 787
Number of extensions: 34
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: 548
Length of database: 531
Length adjustment: 35
Effective length of query: 513
Effective length of database: 496
Effective search space:   254448
Effective search space used:   254448
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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