GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Dinoroseobacter shibae DFL-12

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 3607155 Dshi_0577 aldehyde dehydrogenase (RefSeq)

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



>FitnessBrowser__Dino:3607155
          Length = 483

 Score =  549 bits (1415), Expect = e-161
 Identities = 272/472 (57%), Positives = 341/472 (72%)

Query: 10  YINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSGIQARHD 69
           YI+G W  G     N NPS+ TD IG YA+AD  Q+  A+ AAR A PAW  +GIQ RHD
Sbjct: 8   YIDGAWTEGTAQIENRNPSDTTDLIGMYAQADAGQLDTALAAARRAQPAWWAAGIQKRHD 67

Query: 70  SLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYLPSV 129
            L  +GTE++AR +E+G LL+REEGK L E  GEV RAG  F +FA E LR  GD   SV
Sbjct: 68  VLMAIGTELMARSDEIGRLLSREEGKPLAEGKGEVYRAGQFFTYFAAEALRQHGDLAESV 127

Query: 130 RPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPGCAWALAE 189
           RPG+ ++V REA+GVV +I+PWNFP+A PAWKIAPALA+GN VV KPA++ P  A AL E
Sbjct: 128 RPGIEIDVRREAVGVVAIISPWNFPVATPAWKIAPALAFGNAVVWKPANVTPASAIALTE 187

Query: 190 IISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQL 249
           II+R   P G+FNLV G GR VG  LV+S +VD ISFTGSV VGR IA + V    KVQ+
Sbjct: 188 IIARQDIPKGLFNLVAGPGRDVGQRLVESAEVDAISFTGSVPVGRGIAAAAVQNMTKVQM 247

Query: 250 EMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKFVEAMAERMK 309
           EMG KNP I++DD DL  AV  +  SAF  TGQ+CTA+SR IV + +HD FVE +    +
Sbjct: 248 EMGSKNPLIVMDDCDLDLAVAHAASSAFGGTGQKCTAASRLIVHSAVHDAFVEKLVAAAR 307

Query: 310 SIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDTEGYFLAPTL 369
           ++KVGHAL+ GT +GPVVS++QL Q+++YI +G+ EGA L+ GG  +   T+GYF+AP +
Sbjct: 308 AMKVGHALEDGTQLGPVVSESQLNQNMEYIGVGKDEGAELLCGGDRLEMATDGYFMAPAV 367

Query: 370 FADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSLKYANHFKRH 429
           FA +   MRI+REE+F P+  + RV  Y+ ALA ANDT+FGL+AGI TTSL  A+HF+ H
Sbjct: 368 FAGTANDMRINREEMFAPITAVQRVDSYDEALARANDTQFGLTAGIMTTSLARASHFRAH 427

Query: 430 SQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIGS 481
            +AG VMVNLPTAG DYHVPFGGR  SS+G REQG YA EFYT VKT+Y+ +
Sbjct: 428 MRAGCVMVNLPTAGTDYHVPFGGRGASSFGPREQGSYAAEFYTTVKTAYVAA 479


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: 565
Number of extensions: 15
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: 483
Length adjustment: 34
Effective length of query: 447
Effective length of database: 449
Effective search space:   200703
Effective search space used:   200703
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: 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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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