GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh 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_018413
         (862 letters)



>FitnessBrowser__azobra:AZOBR_RS32240
          Length = 886

 Score = 1009 bits (2610), Expect = 0.0
 Identities = 495/860 (57%), Positives = 654/860 (76%), Gaps = 4/860 (0%)

Query: 1   MKVTTVKELDEKLKVIKEAQKKFSCYSQEMVDEIFRNAAMAAIDARIELAKAAVLETGMG 60
           M VTT+ +L++ +  ++EAQK ++ + QE VD IFR+AA+AA +ARI LAK AV ET MG
Sbjct: 1   MPVTTLADLNDLVLRVREAQKVYAGFPQETVDRIFRSAALAAANARIPLAKLAVAETRMG 60

Query: 61  LVEDKVIKNHFAGEYIYNKYKDEKTCGIIERNEPYGITKIAEPIGVVAAIIPVTNPTSTT 120
           ++EDKV+KNHFA EYIYNKYKDEKTCGI+E +  YGI  IAEP+G++ AI+P TNPTST 
Sbjct: 61  VMEDKVVKNHFASEYIYNKYKDEKTCGILEEDPEYGIMTIAEPVGLICAIVPTTNPTSTA 120

Query: 121 IFKSLISLKTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIGWIDEPSIELTQY 180
           IFK+LISLKTRNGI FSPHPRA+K+T  AA+ +L AAV++GAP +IIGWIDEPS++L+  
Sbjct: 121 IFKALISLKTRNGIVFSPHPRARKATCEAARIVLQAAVEAGAPADIIGWIDEPSVDLSNA 180

Query: 181 LMQKADITL--ATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMAVSSIILSKTY 238
           +M   DI L  ATGGP +VK+AYSSGKPAIGVG GNTP +IDE A IK AV+SI++SKT+
Sbjct: 181 VMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPAVIDEFADIKRAVASILMSKTF 240

Query: 239 DNGVICASEQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIFKDGSVNPKIVGQS 298
           DNGV+CASEQS IV+ ++Y+ V+D F   G +I+   + D VR+V+ K+G++N  IVGQS
Sbjct: 241 DNGVVCASEQSAIVVDAVYDAVRDRFAHHGGHILSGTDADAVRKVLLKNGALNADIVGQS 300

Query: 299 AYTIAAMAGIKVPKTTRILIGEVTSLGEEEPFAHEKLSPVLAMYEADNFDDALKKAVTLI 358
           A  IAAMAG+ VP  T++LI EV ++ E+EPFAHEKLSP LA+Y A +F DA  KA  L+
Sbjct: 301 AGAIAAMAGVSVPANTKVLIAEVEAVTEDEPFAHEKLSPTLALYRARDFMDACDKAAALV 360

Query: 359 NLGGLGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLG 418
            LGG+GHTS +Y D+ +  ++I  F  AMKT R  +N P+SQG  GDLYNFR+ PS TLG
Sbjct: 361 ALGGIGHTSALYTDQDQQPERIRHFGQAMKTARILINTPSSQGGIGDLYNFRLAPSLTLG 420

Query: 419 CGFWGGNSVSENVGPKHLLNIKTVAERRENMLWFRVPHKVYFKFGCLQFALKDLKDLKKK 478
           CG WGGNS+SENVGP+HL+N KTVA+R ENMLW ++P  +YF+ GCL FAL++L+   KK
Sbjct: 421 CGSWGGNSISENVGPQHLINRKTVAKRAENMLWHKLPKSIYFRRGCLPFALEELRG--KK 478

Query: 479 RAFIVTDSDPYNLNYVDSIIKILEHLDIDFKVFNKVGREADLKTIKKATEEMSSFMPDTI 538
           R  IVTD   +   +VD  ++IL+ L +  + F +V  +  L  +++     ++F PD I
Sbjct: 479 RCLIVTDRFLFENGHVDETVRILKGLGLAVETFFEVAADPTLAVVRRGLALANAFQPDVI 538

Query: 539 IALGGTPEMSSAKLMWVLYEHPEVKFEDLAIKFMDIRKRIYTFPKLGKKAMLVAITTSAG 598
           +ALGG   M +AK+MWV+YE P+V FEDLA++FMDIRKRIYTFPKLG KA  VA+ T++G
Sbjct: 539 LALGGGSPMDAAKIMWVMYEAPDVAFEDLALRFMDIRKRIYTFPKLGVKAQFVAVPTTSG 598

Query: 599 SGSEVTPFALVTDNNTGNKYMLADYEMTPNMAIVDAELMMKMPKGLTAYSGIDALVNSIE 658
           +GSEVTPFA+VTD  TG KY +ADYE+TPNMAI+DA L+M MPKGLTA  GIDA+ +++E
Sbjct: 599 TGSEVTPFAVVTDERTGIKYPIADYELTPNMAIIDANLVMDMPKGLTAAGGIDAVTHALE 658

Query: 659 AYTSVYASEYTNGLALEAIRLIFKYLPEAYKNGRTNEKAREKMAHASTMAGMASANAFLG 718
           AY SV A+EYT+G AL+A++L+ ++LP AY NG  + KARE++  A+T+AG+A ANAFLG
Sbjct: 659 AYVSVLANEYTDGQALQALKLLKEHLPSAYANGGKDPKAREQVHSAATLAGIAFANAFLG 718

Query: 719 LCHSMAIKLSSEHNIPSGIANALLIEEVIKFNAVDNPVKQAPCPQYKYPNTIFRYARIAD 778
           +CHSMA KL +E ++P G+ANALLI  VI++NA D P KQ    QY  P  + RYA IA 
Sbjct: 719 VCHSMAHKLGAEFHLPHGVANALLIANVIRYNAADIPTKQTAFSQYDRPKGVARYAEIAR 778

Query: 779 YIKLGGNTDEEKVDLLINKIHELKKALNIPTSIKDAGVLEENFYSSLDRISELALDDQCT 838
           ++ LGG+ D E+V+ L+  + ELK+ L+IP SI+ AGV E  F + LD I+E A DDQCT
Sbjct: 779 HLGLGGSRDHERVETLVAWVEELKRTLDIPASIQAAGVPEAEFLARLDAIAEAAFDDQCT 838

Query: 839 GANPRFPLTSEIKEMYINCF 858
           GANPRFPL +EI+++ ++ +
Sbjct: 839 GANPRFPLVAEIRQLLLDSY 858


Lambda     K      H
   0.317    0.134    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: 1771
Number of extensions: 79
Number of successful extensions: 3
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: 862
Length of database: 886
Length adjustment: 42
Effective length of query: 820
Effective length of database: 844
Effective search space:   692080
Effective search space used:   692080
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 (21.6 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