Alignments for a candidate for paaZ2 in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Methylobacterium nodulans ORS 2060

Align 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase (EC 1.2.1.91) (characterized)
to candidate WP_015929946.1 MNOD_RS15900 phenylacetic acid degradation protein PaaN

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



>NCBI__GCF_000022085.1:WP_015929946.1
          Length = 553

 Score =  519 bits (1336), Expect = e-151
 Identities = 285/550 (51%), Positives = 359/550 (65%), Gaps = 12/550 (2%)

Query: 5   LFTKHEDTLQKALTAVETRGYWSPFVEMPSPKVYGETANADGEAAFKAHLNATFQLDQPS 64
           LF  H   L  A+ A   R +WS F E   PK Y  +A A+G+AAF+A  N  F+L +  
Sbjct: 4   LFQAHAALLDAAVAASRRREFWSAFPE--HPKAYPGSAPAEGQAAFEALKNRPFELARDE 61

Query: 65  TGET----VGAEVSPFGFPLGVRYPKAEPAALIAAAAAAQRDWRAAGPQAWIGVCLEILA 120
             E     VG EVSPFG  LG+ Y       L+AAA  A   W  A  +  +GV LEIL 
Sbjct: 62  QDELRGCWVGEEVSPFGMRLGITYRSQAADDLVAAAQRAHAAWSEASVEQRVGVTLEILV 121

Query: 121 RVNRASFEIGYSVMHTTGQAFMMAFQAGGPHAQDRALEAVVYAWDQLRRIPGDTHWEKPQ 180
           R+N ASF I  +V HTTGQA  MAFQAGGPHAQDR LEAV YA+ ++ R+P    WEKP 
Sbjct: 122 RLNAASFLIAQAVEHTTGQASAMAFQAGGPHAQDRGLEAVAYAYAEMTRVPEAVRWEKPI 181

Query: 181 GKNPPLAMHKRYTVVPRGTGLVLGCCTFPTWNGYPGLFADLATGNTVIVKPHPGAILPLA 240
           G++  + + K + VVPRG GL++GC TFPTWN YP LFA+LATGN VIVKPHP AILPLA
Sbjct: 182 GRSF-IRLDKNFFVVPRGIGLIIGCATFPTWNSYPALFANLATGNAVIVKPHPAAILPLA 240

Query: 241 LTVRIARDVLREAGFDPNVVTLLATEPNDGALVQDLALRPEIKLIDFTGSTQNGTWLERN 300
           LTV+I R+VL   GFDP+V+ L A +  +  L + LA    I ++DFTGS+  G+WL  N
Sbjct: 241 LTVKIGREVLAGQGFDPDVLQL-APDTTEAPLAKILATHAAIDIVDFTGSSAFGSWLRTN 299

Query: 301 AHQAQVYTEKAGVNQIVIDSVDDIKAAARNVAFSLALYSGQMCTAPQNIYVPRGGIRTAE 360
                ++TE+AGVN IVI S +   A  +N+AFSL+LYSGQMCTAPQ I+VP  GI T E
Sbjct: 300 VTDKLLFTEEAGVNTIVIASTNAFSAMCQNIAFSLSLYSGQMCTAPQTIFVPASGISTDE 359

Query: 361 GTLSFDEVAQAIAGAVQKLVADPARAVELLGAIQNEGVTQRIDEAAKLGRVLVESLTLEH 420
           G  SF+ VA +IAGA+  L++DP RA  +LGAIQ+     RI+ A  LGRV+ +S  L  
Sbjct: 360 GHKSFEAVAASIAGAIDALLSDPVRAGAVLGAIQSPETLTRIEAARTLGRVVRDSSAL-- 417

Query: 421 PAFAGARVRTPLVLQLDAATDHAQFTKEWFGPISFVIATDSTAQSLDLAGAIASEHGALT 480
                AR  TPL++ LD A++     +EWFGPI+F++A     + +  A A A   GA+T
Sbjct: 418 -PLERARTATPLLISLD-ASEATPALEEWFGPIAFIVAVHDAEEGIARASAAARTKGAIT 475

Query: 481 LSVYSTDEAVLDDAHEASIRGGVALSINLTGGVFVNQSAAFSDFHGTGANPAANAALADA 540
            ++YSTDEA +  A  +  R GVALS+NLTGG++VNQSAAFSD+H TGANPA NA L D 
Sbjct: 476 AALYSTDEAQIARAIPSYARAGVALSVNLTGGIYVNQSAAFSDYHVTGANPAGNACLTDT 535

Query: 541 AFVANRFRVV 550
           AFVA RFRVV
Sbjct: 536 AFVAGRFRVV 545


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: 808
Number of extensions: 29
Number of successful extensions: 6
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: 553
Length adjustment: 36
Effective length of query: 530
Effective length of database: 517
Effective search space:   274010
Effective search space used:   274010
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 24 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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