Alignments for a candidate for paaH in Azospirillum lipoferum B510

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Azospirillum lipoferum B510

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_012977172.1 AZL_RS24815 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_000010725.1:WP_012977172.1
          Length = 779

 Score =  481 bits (1239), Expect = e-140
 Identities = 304/801 (37%), Positives = 434/801 (54%), Gaps = 40/801 (4%)

Query: 5   IRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLSRQ 64
           I +AAV+G+GVMG+GIAAH AN GIP +LLDI               K+ ++ RS ++R 
Sbjct: 3   IERAAVIGAGVMGAGIAAHFANAGIPCVLLDIP-------------AKEGAD-RSAIARG 48

Query: 65  AMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFALVDE 124
           A+ K+LK  PAP    KN   ITPGNLEDD   L + DWI+E VVEN  +K  ++  +D 
Sbjct: 49  AVAKMLKTDPAPFMHPKNAKLITPGNLEDDLSLLADVDWIVEAVVENPAIKADLYKRIDP 108

Query: 125 HRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDPDIL 184
            RK GS+VSSNTS I +  + EG+ + F   FL THFFNP RY++LLEI+    T PD +
Sbjct: 109 VRKAGSVVSSNTSTIPLAVLTEGQGEQFAKDFLITHFFNPPRYMRLLEIVGGAHTRPDAM 168

Query: 185 KFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGPLIG 244
             +    +  LGKGVV  KDTP FIANRIG   +   V   +  G  V E D++ G  +G
Sbjct: 169 AAIADVCDRRLGKGVVHCKDTPGFIANRIGVLWIQAAVNAAVDLGLTVEEADAVGGRPMG 228

Query: 245 RPKSATFRTLDVVGLDTFAHVARNVYDKADGDE--KEVFRIPSFMNDMLEKGWIGSKAGQ 302
            PK+  F  +D+VGLD   H+A+++       +  +   R    +  M+ +G+ G K   
Sbjct: 229 IPKTGIFGLMDLVGLDLMPHIAKSMSATLPAGDAYRGQMREHPVITKMIAEGYTGRKGKG 288

Query: 303 GFYKKE----GKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRAGR 358
           GFY+      GK    ++  T  Y    K +  ++ AA +       ++ L    D+ GR
Sbjct: 289 GFYRINKTGGGKVKESVNLRTGDYAPSEKARLDSVSAAGR------DLRKLCEHPDKGGR 342

Query: 359 LLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLEQL 418
               + +QTL Y+A L+ EIAD I A+D+ M+ G+ W+ GPFE+ D +G +  AE     
Sbjct: 343 FARRVLAQTLAYAASLVPEIADSIVAVDEGMRLGYNWKQGPFELIDRLGTEWFAELCRAE 402

Query: 419 GADMPGWIKEMLDKGNETFYIKENGTVFYY-DRGEYRAVKENKKRIHLQALKETKG-VIA 476
           G  +P  ++         FY  E G + +    G Y  V      + L  +K   G  + 
Sbjct: 403 GIPVPALVE---TAAGRPFYRVEGGKLQHLTTAGVYDTVVRPDGVLLLSDIKRAAGKPVW 459

Query: 477 KNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLE---ETERNYKGLVIGNQGKNF 533
           KN  ASL D+GD V  +EF SK NA+  DI+    K +    + + ++K LVI N+  NF
Sbjct: 460 KNGSASLWDIGDGVLCVEFTSKMNAVDADIMAAYEKAMRLIGDGKGDWKALVIHNEADNF 519

Query: 534 CVGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLP 593
            VGANL + L  +    + +++ ++   Q T   +KY+  PVVAAP GM LGGG E  L 
Sbjct: 520 SVGANLGLALFALNIGLWPQIEEMVEGGQRTYRALKYAPFPVVAAPSGMALGGGCEILLH 579

Query: 594 AARIQAASEAYMGLVESGVGLIPGGGGNKELYINHL---RRGHDPMNAAMKTFETIAMAK 650
           +  +QA +E Y+GLVE GVGLIP  GG  E+   H    +    PM    K FE I+ A 
Sbjct: 580 SDHVQAHAETYVGLVEVGVGLIPAWGGCTEMLARHQANPKAPRGPMPGTAKAFEIISTAT 639

Query: 651 VSASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKV-PGETGY 709
           V+ SA EA+E+   + TD I++N+D LL DAK  A  L    + PP K    V  G +  
Sbjct: 640 VAKSAAEAKELLYFRATDGITMNRDRLLADAKAKALEL-AANYTPPEKTTSYVLAGPSAK 698

Query: 710 AALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGG-KVPFGTEVDEEYLLEIEREAFLSLS 768
           AA+ L  E   L G ++ HD  +   L+ V++GG +      V E+++L +EREAF+ L 
Sbjct: 699 AAMELAVEGFALQGKVTPHDKLVCAALSEVLSGGEEADISKPVGEDHILRLEREAFMGLV 758

Query: 769 GEAKSQARMQHMLVKGKPLRN 789
               +  R++HML+ GKPLRN
Sbjct: 759 RTGGTIDRIEHMLLTGKPLRN 779


Lambda     K      H
   0.316    0.134    0.382 

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: 1412
Number of extensions: 64
Number of successful extensions: 7
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: 789
Length of database: 779
Length adjustment: 41
Effective length of query: 748
Effective length of database: 738
Effective search space:   552024
Effective search space used:   552024
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources