Alignments for a candidate for paaZ2 in Herbaspirillum autotrophicum IAM 14942

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Herbaspirillum autotrophicum IAM 14942

Align 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase (EC 1.2.1.91) (characterized)
to candidate WP_050462982.1 AKL27_RS11610 phenylacetic acid degradation protein PaaN

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



>NCBI__GCF_001189915.1:WP_050462982.1
          Length = 563

 Score =  725 bits (1872), Expect = 0.0
 Identities = 356/565 (63%), Positives = 437/565 (77%), Gaps = 7/565 (1%)

Query: 1   MTHPLFTKHEDTLQKALTAVETRGYWSPFVEMPSPKVYGETANADGEAAFKAHLNATFQL 60
           M+HP F +H+D LQ+AL A+  RGYWSP+ EMPSP+VYGE+A  DG+AA++A LN  F  
Sbjct: 1   MSHPFFERHQDVLQQALLALTERGYWSPYSEMPSPRVYGESAADDGKAAYEARLNQPFAF 60

Query: 61  D--QPSTGETVGAEVSPFGFPLGVRYPKAEPAALIAAAAAAQRDWRAAGPQAWIGVCLEI 118
              QP  G T G+EVSP+G  LG+ YP  +P  L+ A  AA  +W  AGP+ W GV LEI
Sbjct: 61  HPAQPGNGNTTGSEVSPYGPALGITYPAVDPEQLLPAMHAAAANWYKAGPEVWTGVALEI 120

Query: 119 LARVNRASFEIGYSVMHTTGQAFMMAFQAGGPHAQDRALEAVVYAWDQLRRIPGDTHWEK 178
           ++R+N+ SFEI ++VMHTTGQA+MM+FQAGGPHAQDRA+EA+ YAWD+LRRIPG   WEK
Sbjct: 121 VSRLNQRSFEIAHAVMHTTGQAYMMSFQAGGPHAQDRAVEAIAYAWDELRRIPGQALWEK 180

Query: 179 PQGKNPPLAMHKRYTVVPRGTGLVLGCCTFPTWNGYPGLFADLATGNTVIVKPHPGAILP 238
           PQGKNPPL M K Y VVPRG  LV+GCCTFPTWN YPGLFA LATGN V+VKPHPGAILP
Sbjct: 181 PQGKNPPLRMQKTYRVVPRGLSLVIGCCTFPTWNAYPGLFASLATGNAVLVKPHPGAILP 240

Query: 239 LALTVRIARDVLREAGFDPNVVTLLATEPNDGALVQDLALRPEIKLIDFTGSTQNGTWLE 298
           LA+TV +AR V+ EAGF+P+V+ L A E +  +L  DLALRPE++LIDFTGS  NG WLE
Sbjct: 241 LAITVEVARQVIAEAGFNPDVICLAAHEAS-ASLASDLALRPEVRLIDFTGSAANGNWLE 299

Query: 299 RNAHQAQVYTEKAGVNQIVIDSVDDIKAAARNVAFSLALYSGQMCTAPQNIYVPRGGIRT 358
           ++A QAQV+TEK+GVNQIVIDS  D+    RN+AFSL LYSGQMCTAPQNIY+P  GI T
Sbjct: 300 QHARQAQVFTEKSGVNQIVIDSTADLNGMLRNIAFSLVLYSGQMCTAPQNIYIPAAGIET 359

Query: 359 AEGTLSFDEVAQAIAGAVQKLVADPARAVELLGAIQNEGVTQRIDEAAKLGRVLVESLTL 418
             G LSFD+V  A+  A+ KL  DPA+AVE+LGAIQN  V +RI  A + G ++ +S  L
Sbjct: 360 ETGHLSFDQVVSALGVAIDKLTGDPAKAVEILGAIQNTAVLERIAAARERGEIVTDSRAL 419

Query: 419 EHPAFAGARVRTPLVLQLDAATDHAQFTKEWFGPISFVIATDSTAQSLDLAGAIASEHGA 478
           +HP FAGAR++TPL++++ A       T+E+FGP+SF IAT+ TA S+ +A  IA EHGA
Sbjct: 420 QHPLFAGARIQTPLLIKI-ADVAAKPVTEEYFGPVSFAIATNGTADSIAIAERIAREHGA 478

Query: 479 LTLSVYSTDEAVLDDAHEASIRGGVALSINLTGGVFVNQSAAFSDFHGTGANPAANAALA 538
           LTLS Y+TD+AV +   +A++  GVALS+NL GGVFVNQSAAFSD+HGTGANPAANAAL+
Sbjct: 479 LTLSAYTTDDAVKEQLLDAAVSAGVALSLNLNGGVFVNQSAAFSDYHGTGANPAANAALS 538

Query: 539 DAAFVANRFRVVQSRVHVEPKAAPA 563
           DAAFVA+RFRVVQSR   EP AA A
Sbjct: 539 DAAFVASRFRVVQSR---EPVAAAA 560


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: 893
Number of extensions: 25
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: 566
Length of database: 563
Length adjustment: 36
Effective length of query: 530
Effective length of database: 527
Effective search space:   279310
Effective search space used:   279310
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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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