GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Pseudomonas stutzeri RCH2

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate GFF374 Psest_0375 NAD-dependent aldehyde dehydrogenases

Query= reanno::pseudo1_N1B4:Pf1N1B4_1109
         (481 letters)



>FitnessBrowser__psRCH2:GFF374
          Length = 480

 Score =  771 bits (1992), Expect = 0.0
 Identities = 381/480 (79%), Positives = 422/480 (87%)

Query: 1   VADAKRYDNYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWS 60
           +AD +RYDN+I+G+WV    Y AN NPS+L+D IG+YA+AD AQV  AI AAR AFPAW+
Sbjct: 1   MADVQRYDNFIDGQWVGSDRYQANTNPSDLSDVIGEYAQADAAQVEQAIAAARRAFPAWA 60

Query: 61  TSGIQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLR 120
           T GIQAR D+L+KVG EILARREELGTLLAREEGKTLPEAIGEV RAGNIFK+FAGECLR
Sbjct: 61  TFGIQARADALEKVGLEILARREELGTLLAREEGKTLPEAIGEVARAGNIFKYFAGECLR 120

Query: 121 LSGDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLV 180
            +G+ L SVRPGV VEVTRE LGV+GLITPWNFPIAIPAWKIAPALA+GNCVV+KPADLV
Sbjct: 121 QAGETLQSVRPGVGVEVTREPLGVIGLITPWNFPIAIPAWKIAPALAFGNCVVIKPADLV 180

Query: 181 PGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSC 240
           PGCAWA+AEIISRAGFPAGVFNLVMG GR VG+A+V +  VD +SFTGSVGVGR IA +C
Sbjct: 181 PGCAWAIAEIISRAGFPAGVFNLVMGKGREVGEAIVNAKDVDAVSFTGSVGVGRGIAQTC 240

Query: 241 VSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKF 300
           V+R AKVQLEMGGKNPQI+LDDADL  AVEL  QSAFYSTGQRCTASSR IVT GI+D+F
Sbjct: 241 VARGAKVQLEMGGKNPQIVLDDADLNVAVELCTQSAFYSTGQRCTASSRIIVTEGIYDRF 300

Query: 301 VEAMAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDT 360
           VEAM ER+K IKVG AL+ G D+GPVVS+AQLEQDL+YI+IG+ EGARL  GG  V C T
Sbjct: 301 VEAMVERIKKIKVGSALEQGVDVGPVVSEAQLEQDLRYIEIGKQEGARLACGGERVKCGT 360

Query: 361 EGYFLAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSL 420
           EGYFLAPTLF DS   MRISREEIFGPVAN+V+V DY+ ALAMANDTEFGLSAGI TTSL
Sbjct: 361 EGYFLAPTLFVDSDPNMRISREEIFGPVANVVKVKDYDEALAMANDTEFGLSAGICTTSL 420

Query: 421 KYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIG 480
           KYANHFKRH+QAGMVM+NLPTAGVDYHVPFGGRKGSSYG REQGRYAQEFYT VKT+YIG
Sbjct: 421 KYANHFKRHAQAGMVMINLPTAGVDYHVPFGGRKGSSYGPREQGRYAQEFYTTVKTTYIG 480


Lambda     K      H
   0.318    0.134    0.391 

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: 761
Number of extensions: 18
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: 481
Length of database: 480
Length adjustment: 34
Effective length of query: 447
Effective length of database: 446
Effective search space:   199362
Effective search space used:   199362
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: 51 (24.3 bits)

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

Links

Downloads

Related tools

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