Alignments for a candidate for paaZ2 in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Cupriavidus basilensis 4G11

Align 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase (EC 1.2.1.91) (characterized)
to candidate RR42_RS23750 RR42_RS23750 aldehyde dehydrogenase

Query= reanno::BFirm:BPHYT_RS17340
         (566 letters)



>FitnessBrowser__Cup4G11:RR42_RS23750
          Length = 560

 Score =  832 bits (2148), Expect = 0.0
 Identities = 417/556 (75%), Positives = 465/556 (83%)

Query: 1   MTHPLFTKHEDTLQKALTAVETRGYWSPFVEMPSPKVYGETANADGEAAFKAHLNATFQL 60
           M H LF KHE TL +AL A+ TRGYWSPF EMPSP+ YGETA ADGEAAFKA L   F L
Sbjct: 1   MNHALFEKHEKTLAQALDAIRTRGYWSPFNEMPSPRTYGETAAADGEAAFKAQLGQPFVL 60

Query: 61  DQPSTGETVGAEVSPFGFPLGVRYPKAEPAALIAAAAAAQRDWRAAGPQAWIGVCLEILA 120
           +Q  +  TVGAE SPFGF L + YP AEP ALIAAA AAQ  +R AGP+AW+GV LEILA
Sbjct: 61  EQAGSSGTVGAEHSPFGFALNIGYPNAEPDALIAAAQAAQLQFRKAGPKAWVGVSLEILA 120

Query: 121 RVNRASFEIGYSVMHTTGQAFMMAFQAGGPHAQDRALEAVVYAWDQLRRIPGDTHWEKPQ 180
           R+N+ASFEI +SVMHTTGQAFMMAFQAGGPHAQDRALEA+ YAWD +R IP   +WEKPQ
Sbjct: 121 RLNQASFEIAHSVMHTTGQAFMMAFQAGGPHAQDRALEAIAYAWDAMRDIPQTAYWEKPQ 180

Query: 181 GKNPPLAMHKRYTVVPRGTGLVLGCCTFPTWNGYPGLFADLATGNTVIVKPHPGAILPLA 240
           GKNPPLAM KR+TVVPRG GLV+GCCTFPTWN YPGLFADLATGN VIVKPHP AILPLA
Sbjct: 181 GKNPPLAMEKRFTVVPRGIGLVIGCCTFPTWNSYPGLFADLATGNAVIVKPHPAAILPLA 240

Query: 241 LTVRIARDVLREAGFDPNVVTLLATEPNDGALVQDLALRPEIKLIDFTGSTQNGTWLERN 300
           +TVRIAR VL EAGFDPNVVTL+AT PNDGALVQ LA R EI+LIDFTGST NG WLE +
Sbjct: 241 ITVRIARQVLEEAGFDPNVVTLMATAPNDGALVQALATRDEIRLIDFTGSTANGDWLETH 300

Query: 301 AHQAQVYTEKAGVNQIVIDSVDDIKAAARNVAFSLALYSGQMCTAPQNIYVPRGGIRTAE 360
           A QAQVYTEKAGVNQIVIDS D++KA +RN+AFSLALYSGQMCTAPQNIYVPR GI+TA+
Sbjct: 301 ALQAQVYTEKAGVNQIVIDSADELKAVSRNIAFSLALYSGQMCTAPQNIYVPRDGIKTAQ 360

Query: 361 GTLSFDEVAQAIAGAVQKLVADPARAVELLGAIQNEGVTQRIDEAAKLGRVLVESLTLEH 420
           GT+ F+EVAQ+IA AVQKL +DPA+AVEL+GAIQN+GV  RI++  KLG  L+ S  L H
Sbjct: 361 GTVPFEEVAQSIADAVQKLTSDPAKAVELIGAIQNKGVLDRIEQVTKLGVPLLASQRLVH 420

Query: 421 PAFAGARVRTPLVLQLDAATDHAQFTKEWFGPISFVIATDSTAQSLDLAGAIASEHGALT 480
           PA+  A V TP++L+LDA  D   FT+EWFGPI+FVIATDST  SL+LA  IA   GALT
Sbjct: 421 PAYPEASVSTPVLLKLDARRDEDTFTQEWFGPIAFVIATDSTRHSLELAARIARTRGALT 480

Query: 481 LSVYSTDEAVLDDAHEASIRGGVALSINLTGGVFVNQSAAFSDFHGTGANPAANAALADA 540
           LSVYSTDE VLD A EA++ GGVALS+NLTGGVFVNQSAAFSDFH TGANPAANA+LAD 
Sbjct: 481 LSVYSTDEQVLDAADEAAVSGGVALSVNLTGGVFVNQSAAFSDFHATGANPAANASLADT 540

Query: 541 AFVANRFRVVQSRVHV 556
           AFVANRFRVVQSR HV
Sbjct: 541 AFVANRFRVVQSRRHV 556


Lambda     K      H
   0.318    0.133    0.394 

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: 874
Number of extensions: 20
Number of successful extensions: 1
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: 566
Length of database: 560
Length adjustment: 36
Effective length of query: 530
Effective length of database: 524
Effective search space:   277720
Effective search space used:   277720
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: 53 (25.0 bits)

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

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Candidates (tab-delimited)
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