GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS32240
          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:

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