GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ald-dh-CoA in Azospirillum brasilense Sp245

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate AZOBR_RS32240 AZOBR_RS32240 acetaldehyde dehydrogenase

Query= CharProtDB::CH_024820
         (891 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS32240 AZOBR_RS32240 acetaldehyde
           dehydrogenase
          Length = 886

 Score = 1327 bits (3435), Expect = 0.0
 Identities = 661/886 (74%), Positives = 766/886 (86%), Gaps = 8/886 (0%)

Query: 1   MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60
           M VT +A+LN LV RV++AQ+ YA F QE VD+IFR+AALAAA+ARIPLAK+AVAE+ MG
Sbjct: 1   MPVTTLADLNDLVLRVREAQKVYAGFPQETVDRIFRSAALAAANARIPLAKLAVAETRMG 60

Query: 61  IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120
           ++EDKV+KNHFASEYIYN YKDEKTCG+L ED  +G +TIAEP+G+IC IVPTTNPTSTA
Sbjct: 61  VMEDKVVKNHFASEYIYNKYKDEKTCGILEEDPEYGIMTIAEPVGLICAIVPTTNPTSTA 120

Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180
           IFK+LISLKTRN I+FSPHPRA+ AT +AA IVLQAA+ AGAP D+IGWID+PSV+LSNA
Sbjct: 121 IFKALISLKTRNGIVFSPHPRARKATCEAARIVLQAAVEAGAPADIIGWIDEPSVDLSNA 180

Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240
           +MHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTP VIDE ADIKRAVAS+LMSKTF
Sbjct: 181 VMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPAVIDEFADIKRAVASILMSKTF 240

Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300
           DNGV+CASEQS +VVD+VYDAVR+RFA HGG++L G +  AV+ V+LKNGALNA IVGQ 
Sbjct: 241 DNGVVCASEQSAIVVDAVYDAVRDRFAHHGGHILSGTDADAVRKVLLKNGALNADIVGQS 300

Query: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360
           A  IA +AG SVP NTK+LI EV  V E EPFAHEKLSPTLA+YRA+DF DA +KA  LV
Sbjct: 301 AGAIAAMAGVSVPANTKVLIAEVEAVTEDEPFAHEKLSPTLALYRARDFMDACDKAAALV 360

Query: 361 AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420
           A+GGIGHTS LYTDQD QP R+ +FGQ MKTARILINTP+SQGGIGDLYNF+LAPSLTLG
Sbjct: 361 ALGGIGHTSALYTDQDQQPERIRHFGQAMKTARILINTPSSQGGIGDLYNFRLAPSLTLG 420

Query: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK 480
           CGSWGGNSISENVGP+HLIN+KTVAKRAENMLWHKLPKSIYFRRG LP AL+E+   G K
Sbjct: 421 CGSWGGNSISENVGPQHLINRKTVAKRAENMLWHKLPKSIYFRRGCLPFALEEL--RGKK 478

Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540
           R LIVTDRFLF NG+ D+   +LK  G+  E FFEV ADPTL++VR+G  LAN+F+PDVI
Sbjct: 479 RCLIVTDRFLFENGHVDETVRILKGLGLAVETFFEVAADPTLAVVRRGLALANAFQPDVI 538

Query: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600
           +ALGGGSPMDAAKIMWVMYE P+  FE+LALRFMDIRKRIY FPK+GVKA+ +AV TTSG
Sbjct: 539 LALGGGSPMDAAKIMWVMYEAPDVAFEDLALRFMDIRKRIYTFPKLGVKAQFVAVPTTSG 598

Query: 601 TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME 660
           TGSEVTPFAVVTD+ TG KYP+ADY LTP+MAI+DANLVMDMPK L A GG+DAVTHA+E
Sbjct: 599 TGSEVTPFAVVTDERTGIKYPIADYELTPNMAIIDANLVMDMPKGLTAAGGIDAVTHALE 658

Query: 661 AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720
           AYVSVLA+E++DGQALQALKLLKE+LP++Y  G K+P ARE+VHSAAT+AGIAFANAFLG
Sbjct: 659 AYVSVLANEYTDGQALQALKLLKEHLPSAYANGGKDPKAREQVHSAATLAGIAFANAFLG 718

Query: 721 VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780
           VCHSMAHKLG++FH+PHG+ANALLI NVIRYNA D PTKQTAFSQYDRP+   RYAEIA 
Sbjct: 719 VCHSMAHKLGAEFHLPHGVANALLIANVIRYNAADIPTKQTAFSQYDRPKGVARYAEIAR 778

Query: 781 HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ 840
           HLGL   G R   ++E L+AW+E LK  L IP SI+ AGV EA+FLA +D ++E AFDDQ
Sbjct: 779 HLGLG--GSRDHERVETLVAWVEELKRTLDIPASIQAAGVPEAEFLARLDAIAEAAFDDQ 836

Query: 841 CTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKK 886
           CTGANPR+PL++E++Q+LLD+YYGR Y EG   A++E   AKAE+K
Sbjct: 837 CTGANPRFPLVAEIRQLLLDSYYGRAYAEG---AERE-PDAKAERK 878


Lambda     K      H
   0.317    0.132    0.378 

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: 1905
Number of extensions: 63
Number of successful extensions: 5
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: 891
Length of database: 886
Length adjustment: 43
Effective length of query: 848
Effective length of database: 843
Effective search space:   714864
Effective search space used:   714864
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: 56 (26.2 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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